Initial commit - 18/6/2018

.gitignore

+BLAST/dbs
+BLAST/rat-ests
+FreeSurfer/buckner_data
+FreeSurfer/buckner_data-tutorial_subjs.tar.gz
+FSL/intro
+FSL/preCourse.tar.gz
+FSL/fmri
+Gaussian/g16
+Gaussian/tests
+HPCshells/NAMD
+NAMD/apoa1
+NAMD/NAMD_BENCHMARKS_SPARTAN
+NAMD/stmv
+Python/minitwitter.csv
+Singularity/vsoch-hello-world-master.simg
+

ANSYS/README.md

+Please note that this tutorial is not complete yet!

ANSYS/ansys.slurm

+#!/bin/bash
+# SBATCH --account=punim0396 
+# SBATCH --partition=punim0396
+#SBATCH --job-name="ANSYS test"
+#SBATCH --partition=physical-cx4
+#SBATCH --ntasks=1
+#SBATCH --time=0-00:10:00
+#SBATCH --gres=aa_r+1%aa_r_hpc+12
+
+module load ansys/19.0-intel-2017.u2
+
+ansys19 -b < OscillatingPlate.inp > OscillatingPlate.db

ANSYS/pbs-cfx-benchmark

+#!/bin/bash
+
+#     	job name:
+#PBS -N ansys_benchmark
+
+#     	how many cpus?
+#PBS -l nodes=1:ppn=2
+
+#     	How long to run the job? (hours:minutes:seconds)
+#       You will almost certainly need to change this.
+#PBS -l walltime=00:15:00
+
+#       Wait for license file
+#       Please leave this as it is, makes it a lot safer.
+# PBS -W x=gres:aa_r+1
+#PBS -W x=GRES:aa_r+1%aa_r_hpc+2
+
+#     	Environmental varibles to make it work:
+
+module load ansys/145
+
+cd $PBS_O_WORKDIR
+ 
+# Launching the job!
+
+NODES=$(cat $PBS_NODEFILE | sort | uniq -c | awk '{print $2 "*" $1}' | tr '\n' ',' | sed 's/,$//')
+
+echo "This job is allocated on $NODES"
+
+cfx5solve  -def Benchmark.def -parallel -par-dist $NODES

ANSYS/pbs-script-cfx

+#!/bin/bash
+
+# ------------------------------------
+#       ANSYS - CFX FSI script.
+#       All you need change is wall time and name of input files.
+#       And possibly the job name.
+# -----------------------------------
+
+# 	pbs launching script example for ANSYS job:
+
+#     	job name: --- Change this if you like
+#PBS -N ansys_job_01
+
+#     	how many cpus? --- Probably best choice.
+#PBS -l nodes=8
+
+#     	How long to run the job? (hours:minutes:seconds)
+#       You will almost certainly need to change this.
+#PBS -l walltime=00:30:00
+
+#     	Name of output file:
+# PBS -o ansys_test_job_02.txt
+
+#       Wait for license file
+#       Please leave this as it is, makes it a lot safer.
+# PBS -l software=aa_r+1
+#PBS -W x=GRES:aa_r+1%aa_r_hpc+2
+
+#	For CFX use only
+# PBS -l software=cfx_par_proc+8
+
+#     	Environmental varibles to make it work:
+
+  module load ansys/145
+
+  cd $PBS_O_WORKDIR
+ 
+#     	Launching the job!
+
+NODES=$(cat $PBS_NODEFILE | sort | uniq -c | awk '{print $2 "*" $1}' | tr '\n' ',' | sed 's/,$//')
+
+echo "This job is allocated on $NODES"
+
+cfx5solve  -def  OscillatingPlate.def -ansys-input  OscillatingPlate.inp -parallel -par-dist $NODES

BLAST/README

+Rattus Norvegicus 
+=================
+
+Sequence files and rat ESTs with BLAST
+--------------------------------------
+
+1. Get fasta nucleic acid (fna) FASTA formatted sequence files for Rattus Norvegicus
+
+wget ftp://ftp.ncbi.nih.gov/refseq/R_norvegicus/mRNA_Prot/rat.1.rna.fna.gz
+
+gunzip rat.1.rna.fna.gz
+
+formatdb -i rat.1.rna.fna -p F -o T
+
+2. Get the Express Sequence Tags, a short sub-sequence of cDNA sequence used to identify gene transcripts, used for gene discovery and gene-sequence determination
+
+wget http://mirrors.vbi.vt.edu/mirrors/ftp.ncbi.nih.gov/genomes/Rattus_norvegicus/ARCHIVE/2002/rn_est.gz
+
+gunzip rn_est
+
+3. Run Slurm script to BLAST
+

BLAST/blast.slurm

+#!/bin/bash
+
+# Set the partition
+
+#SBATCH -p cloud 
+
+# Set the number of processors that will be used.
+#SBATCH --nodes=1
+#SBATCH --ntasks-per-node=8
+
+# Set the walltime (10 hrs)
+
+#SBATCH --time=10:00:00
+
+# Load the environment variables
+
+module load BLAST/2.2.26-Linux_x86_64
+
+# Run the job
+
+blastall -i ./rat-ests/rn_est -d ./dbs/rat.1.rna.fna -p blastn -e 0.05 -v 5 -b 5 -T F -m 9 -o rat_blast_tab.txt -a 8

COMSOL/comsol.slurm

+#!/bin/bash
+#SBATCH --time=24:00:00
+#SBATCH --nodes=1
+#SBATCH --ntasks-per-node=8
+# You might need an external license file
+# export LM_LICENSE_FILE=port@licenseserver
+ 
+module load COMSOL/5.2
+
+# Example batch command from csiro.org.au
+comsol batch -inputfile mymodel.mph  -outputfile mymodelresult.mph -batchlog mybatch.log -j b1 -np 8 -mpmode owner

FDS/FDS.slurm

+#!/bin/bash
+
+#SBATCH --job-name FDS_example_job
+
+#How many nodes/cores? FDS is MPI enabled and can operate across multiple nodes
+
+#SBATCH --nodes=1
+#SBATCH --ntasks-per-node=4
+
+#What is the maximum time this job is expected to take? (Walltime) 
+#Format: Days-Hours:Minutes:Seconds
+
+#SBATCH --time=1-24:00:00
+
+module load FDS
+
+fds inputfile.fds outputfile.fds 

FSL/FSLsample1.slurm

+#!/bin/bash
+
+#SBATCH -p cloud
+
+#SBATCH --ntasks=1
+
+#SBATCH -t 0:15:00
+
+module load FSL/5.0.9-centos6_64 
+
+# FSL needs to be sourced
+source $FSLDIR/etc/fslconf/fsl.sh
+
+srun bet /usr/local/common/FSL/intro/structural.nii.gz test1FSL -f 0.1
+

FSL/FSLsample2.slurm

+#!/bin/bash
+#SBATCH -p cloud
+#SBATCH --ntasks=8
+#SBATCH -t 0:00:05
+
+module load FSL/5.0.9-centos6_64 
+
+# FSL needs to be sourced
+source $FSLDIR/etc/fslconf/fsl.sh
+
+srun -n 8 bet /usr/local/common/FSL/intro/structural.nii.gz test2FSL -f 0.1
+

FreeSurfer/FreeSurfer1.slurm

+#!/bin/bash
+#SBATCH -p cloud
+#SBATCH --ntasks=1
+#SBATCH -t 00:15:00
+
+module load FreeSurfer/5.3.0-GCC-4.9.2-centos6_x86_64
+
+# Tutorial derived from `https://surfer.nmr.mgh.harvard.edu/fswiki/FsTutorial/GroupAnalysis`
+
+# Export directories
+export TUTORIAL_DATA=/usr/local/common/FreeSurfer
+export SUBJECTS_DIR=$TUTORIAL_DATA/buckner_data/tutorial_subjs/group_analysis_tutorial
+
+# Create contrast; test the change in thickness with age, after removing the effects of gender.
+echo "0 0 0.5 0.5" > lh-Avg-thickness-age-Cor.mtx
+
+# Assemble the precached Data (mris_preproc)
+
+mris_preproc --fsgd $SUBJECTS_DIR/glm/gender_age.fsgd --cache-in thickness.fwhm10.fsaverage --target fsaverage  --hemi lh --out lh.gender_age.thickness.10.mgh
+
+# Assemble the data (non-cached)
+# mris_preproc --fsgd $SUBJECTS_DIR/glm/gender_age.fsgd --target fsaverage --hemi lh --meas thickness --out $SUBJECTS_DIR/glm/lh.gender_age.thickness.00.mg
+
+# mri_surf2surf --hemi lh --s fsaverage --sval lh.gender_age.thickness.00.mgh --fwhm 10 --cortex --tval lh.gender_age.thickness.10B.mgh
+
+mri_glmfit --y lh.gender_age.thickness.10.mgh --fsgd $SUBJECTS_DIR/glm/gender_age.fsgd dods --C $SUBJECTS_DIR/glm/lh-Avg-thickness-age-Cor.mtx --surf fsaverage lh --cortex --glmdir lh.gender_age.glmdir
+
+
+

FreeSurfer/README

+We don't have the complete set of libraries installed (yet) on the compute nodes for FreeSurfer visualisation. In the meantime, short visualisation sessions can be conducted on the login node. As always, it is better to do visualisation locally and computation on the cluster.
+
+The following is an example session for visualisation.
+
+[lev@cricetomys HPCshells]$ ssh spartan -Y
+..
+[lev@spartan ~]$ module load FreeSurfer/6.0.0-GCC-4.9.2-centos6_x86_64
+[lev@spartan ~]$ module load X11/20160819-GCC-4.9.2
+[lev@spartan ~]$ export TUTORIAL_DATA=/usr/local/common/FreeSurfer
+[lev@spartan ~]$ export SUBJECTS_DIR=$TUTORIAL_DATA/buckner_data/tutorial_subjs
+[lev@spartan ~]$ cd $SUBJECTS_DIR
+[lev@spartan ~]$ freeview -v \
+good_output/mri/T1.mgz \
+good_output/mri/wm.mgz \
+good_output/mri/brainmask.mgz \
+good_output/mri/aseg.mgz:colormap=lut:opacity=0.2 \
+-f good_output/surf/lh.white:edgecolor=blue \
+good_output/surf/lh.pial:edgecolor=red \
+good_output/surf/rh.white:edgecolor=blue \
+good_output/surf/rh.pial:edgecolor=red
+
+See more here to continue the tutorial:
+
+https://surfer.nmr.mgh.harvard.edu/fswiki/FsTutorial/OutputData_freeview
+
+
+
+

GPU/README

+# This directory contains a sample Slurm scripts for the use of GPUs on Spartan. The main difference between submitting a standard Slurm job and a job that makes use of GPUs is additional paramters to the Slurm script. A user will need to specifiy that the GPU partition is being used and, in addition, a generic resource (GRES) resource request hhas been specified and the quantity of GPUs being requested.
+
+#SBATCH --partition gpu 
+#SBATCH --gres=gpu 
+
+# One can also select instead, if you have access:
+#
+#SBATCH --partition gpgpu
+
+# For example if you wish to access up four GPUs in a single job use:
+
+#SBATCH --gres=gpu:4.
+
+# However, note that this is for any type of GPGPU. However we have different GPGPUs installed. This will need to be specified.
+#
+# For example if you submit a job that says `--gres=gpu` for 1 GPU or `--gres=gpu:2` for 2 GPUs per task then that can be satisfied by either type
+# but if you need a specific type (say P100) then you need to submit with `--gres=gpu:p100` and if you need 2 per task then you would do `--gres=gpu:p100:2`.
+
+
+# Derived from:
+# https://stackoverflow.com/questions/7663343/simplest-possible-example-to-show-gpu-outperform-cpu-using-cuda
+
+# "GPUs are high bandwidth, high latency. Trying to get the GPU to beat a CPU for a nanosecond job (or even a millisecond or second job) is 
+# completely missing the point of doing GPU stuff. Below is some simple code, but to really appreciate the performance benefits of GPU, you'll 
+# need a big problem size to amortize the startup costs over... otherwise, it's meaningless. I can beat a Ferrari in a two foot race, simply 
+# because it take some time to turn the key, start the engine and push the pedal. That doesn't mean I'm faster than the Ferrari in any 
+# meaningful way."
+
+[lev@spartan ~]$ sinteractive --time=0:30:0 
+srun: job 1191791 queued and waiting for resources
+srun: job 1191791 has been allocated resources
+[lev@spartan-rc024 ~]$ module load CUDA/7.5.18-GCC-4.9.2
+
+# Note, must use -std=gnu99 or similar
+
+[lev@spartan-rc024 ~]$ gcc ferrari.c -std=gnu99 -o ferrari
+[lev@spartan-rc024 ~]$ time ./ferrari
+Enter an index: 33
+data[33] = -0.207107
+
+real	0m22.516s
+user	0m19.933s
+sys	0m0.004s
+
+[lev@spartan ~]$ sinteractive --time=0:30:0 --partition=gpu --gres=gpu:1
+srun: job 1191798 queued and waiting for resources
+srun: job 1191798 has been allocated resources
+[lev@spartan-gpu005 ~]$ nvcc ferrari.cu -o ferrari_gpu 
+[lev@spartan-gpu005 ~]$ time ./ferrari_gpu
+Enter an index: 33
+data[33] = 0.000000
+
+real	0m1.112s
+user	0m0.001s
+sys	0m0.015s
+[lev@spartan-gpu005 GPU]$
+ 

GPU/addition.cu

+#include <stdio.h>
+
+__global__ void add(int *a, int *b, int *c) 
+	{
+	*c = *a + *b;
+	}
+
+int main(void) 
+	{
+	int a, b, c; // host copies of a, b, c
+	int *d_a, *d_b, *d_c; // device copies of a, b, c
+	int size = sizeof(int);
+
+	// Allocate space for device copies of a, b, c
+	cudaMalloc((void **)&d_a, size);
+	cudaMalloc((void **)&d_b, size);
+	cudaMalloc((void **)&d_c, size);
+
+	// Setup input values
+	a = 2;
+	b = 7;
+	c = 0;
+
+	// Copy inputs to device
+	cudaMemcpy(d_a, &a, size, cudaMemcpyHostToDevice);
+	cudaMemcpy(d_b, &b, size, cudaMemcpyHostToDevice);
+
+	// Launch add() kernel on GPU
+	add<<<1,1>>>(d_a, d_b, d_c);
+
+	// Copy result back to host
+	cudaMemcpy(&c, d_c, size, cudaMemcpyDeviceToHost);
+	
+	// Print variable
+	printf("%d\n", d_c);
+
+	// Cleanup
+	cudaFree(d_a); cudaFree(d_b); cudaFree(d_c);
+
+
+	return 0;
+	}
+

GPU/beetle.c

+#include <stdio.h>
+#define N (16*16)
+#define M (20)
+int main()
+     {
+     float data[N]; int count = 0;
+     for(int i = 0; i < N; i++)
+     {
+        data[i] = 1.0f * i / N;
+        for(int j = 0; j < M; j++)
+        {
+           data[i] = data[i] * data[i] - 0.25f;
+        }
+     }
+     int sel;
+     printf("Enter an index: ");
+     scanf("%d", &sel);
+     printf("data[%d] = %f\n", sel, data[sel]);
+  }

GPU/beetle.cu

+#include <stdio.h> 
+#define N (16*16)
+#define M (20)
+
+  __global__ void cudakernel(float *buf)
+  {
+     int i = threadIdx.x + blockIdx.x * blockDim.x;
+     buf[i] = 1.0f * i / N;
+     for(int j = 0; j < M; j++)
+        buf[i] = buf[i] * buf[i] - 0.25f;
+  }
+
+  int main()
+  {
+     float data[N];
+     float *d_data;
+     cudaMalloc(&d_data, N * sizeof(float));
+     cudakernel<<<N/32, 32>>>(d_data);
+     cudaMemcpy(data, d_data, N * sizeof(float), cudaMemcpyDeviceToHost);
+     cudaFree(d_data); 
+
+     int sel;
+     printf("Enter an index: ");
+     scanf("%d", &sel);
+     printf("data[%d] = %f\n", sel, data[sel]);
+  }
+

GPU/ferrari.c

+#include <stdio.h>
+
+#define N (512*512)
+#define M (10000)
+int main()
+     {
+     float data[N]; int count = 0;
+     for(int i = 0; i < N; i++)
+     {
+        data[i] = 1.0f * i / N;
+        for(int j = 0; j < M; j++)
+        {
+           data[i] = data[i] * data[i] - 0.25f;
+        }
+     }
+     int sel;
+     printf("Enter an index: ");
+     scanf("%d", &sel);
+     printf("data[%d] = %f\n", sel, data[sel]);
+  }

GPU/ferrari.cu

+#include <stdio.h> 
+#define N (512*512)
+#define M (10000)
+
+  __global__ void cudakernel(float *buf)
+  {
+     int i = threadIdx.x + blockIdx.x * blockDim.x;
+     buf[i] = 1.0f * i / N;
+     for(int j = 0; j < M; j++)
+        buf[i] = buf[i] * buf[i] - 0.25f;
+  }
+
+  int main()
+  {
+     float data[N];
+     float *d_data;
+     cudaMalloc(&d_data, N * sizeof(float));
+     cudakernel<<<N/256, 256>>>(d_data);
+     cudaMemcpy(data, d_data, N * sizeof(float), cudaMemcpyDeviceToHost);
+     cudaFree(d_data); 
+
+     int sel;
+     printf("Enter an index: ");
+     scanf("%d", &sel);
+     printf("data[%d] = %f\n", sel, data[sel]);
+  }
+

GPU/hello.cu

+#include <stdio.h>
+
+int main(void) 
+	{
+	printf("Hello World!\n");
+	return 0;
+	}

GPU/hello2.cu

+#include <stdio.h>
+
+__global__ void mykernel(void) 
+	{
+	}
+
+int main(void) 
+	{
+	mykernel<<<1,1>>>();
+	printf("Hello World!\n");
+	return 0;
+	}
+
+

GPU/profile.slurm

+# This will profile your application using the default CUDA counters, if 
+# you would like to use different counter you can specify this by using 
+# CUDA_PROFILE_CONFIG environment variable which points to a file 
+# containing the counters you want to use (limited to 4 per run), you 
+# can find more information regarding the counters and the config file 
+# on the NVIDIA cuda documentation. 
+#
+# Please be aware that the profiler will only sample from 1 GPU, it has 
+# the same limitations as the nVidia Visual profiler provided in the 
+# CUDA toolkit.
+
+declare CUDA_PROFILE=1
+declare CUDA_PROFILE_CSV=1
+declare CUDA_PROFILE_LOG=$HOSTNAME.nvidia.profiler.output
+
+declare -x CUDA_PROFILE
+declare -x CUDA_PROFILE_CSV
+declare -x CUDA_PROFILE_LOG
+

GROMACS/gmxdemo/cpeptide.pdb

+ATOM      1  N   LYS     1      24.966  -0.646  22.314  1.00 32.74      1SRN  99
+ATOM      2  CA  LYS     1      24.121   0.549  22.271  1.00 32.05      1SRN 100
+ATOM      3  C   LYS     1      24.794   1.733  22.943  1.00 31.16      1SRN 101
+ATOM      4  O   LYS     1      25.742   1.575  23.764  1.00 31.50      1SRN 102
+ATOM      5  CB  LYS     1      22.812   0.323  23.047  1.00 33.09      1SRN 103
+ATOM      6  CG  LYS     1      21.763   1.415  22.695  1.00 34.29      1SRN 104
+ATOM      7  CD  LYS     1      20.497   1.124  23.561  1.00 34.93      1SRN 105
+ATOM      8  CE  LYS     1      20.706   1.659  24.970  1.00 35.35      1SRN 106
+ATOM      9  NZ  LYS     1      21.524   0.759  25.825  1.00 35.85      1SRN 107
+ATOM     10  N   GLU     2      24.300   2.909  22.632  1.00 29.30      1SRN 108
+ATOM     11  CA  GLU     2      24.858   4.145  23.207  1.00 27.38      1SRN 109
+ATOM     12  C   GLU     2      24.567   4.201  24.693  1.00 26.12      1SRN 110
+ATOM     13  O   GLU     2      23.398   4.051  25.038  1.00 26.39      1SRN 111
+ATOM     14  CB  GLU     2      24.238   5.355  22.537  1.00 27.12      1SRN 112
+ATOM     15  CG  GLU     2      24.775   6.731  22.894  1.00 26.16      1SRN 113
+ATOM     16  CD  GLU     2      24.277   7.798  21.950  1.00 25.53      1SRN 114
+ATOM     17  OE1 GLU     2      23.087   7.974  21.734  1.00 25.09      1SRN 115
+ATOM     18  OE2 GLU     2      25.200   8.451  21.448  1.00 24.78      1SRN 116
+ATOM     19  N   THR     3      25.608   4.399  25.499  1.00 24.80      1SRN 117
+ATOM     20  CA  THR     3      25.475   4.513  26.954  1.00 23.26      1SRN 118
+ATOM     21  C   THR     3      24.803   5.847  27.263  1.00 22.23      1SRN 119
+ATOM     22  O   THR     3      24.805   6.756  26.419  1.00 22.26      1SRN 120
+ATOM     23  CB  THR     3      26.857   4.478  27.708  1.00 23.53      1SRN 121
+ATOM     24  OG1 THR     3      27.581   5.698  27.276  1.00 23.39      1SRN 122
+ATOM     25  CG2 THR     3      27.750   3.260  27.496  1.00 23.71      1SRN 123
+ATOM     26  N   ALA     4      24.316   6.023  28.470  1.00 20.81      1SRN 124
+ATOM     27  CA  ALA     4      23.646   7.264  28.928  1.00 19.56      1SRN 125
+ATOM     28  C   ALA     4      24.622   8.442  28.958  1.00 18.79      1SRN 126
+ATOM     29  O   ALA     4      24.267   9.606  28.686  1.00 17.61      1SRN 127
+ATOM     30  CB  ALA     4      23.015   7.064  30.281  1.00 19.62      1SRN 128
+ATOM     31  N   ALA     5      25.824   8.089  29.315  1.00 18.22      1SRN 129
+ATOM     32  CA  ALA     5      26.973   9.001  29.411  1.00 18.17      1SRN 130
+ATOM     33  C   ALA     5      27.301   9.459  27.996  1.00 18.37      1SRN 131
+ATOM     34  O   ALA     5      27.487  10.671  27.734  1.00 18.89      1SRN 132
+ATOM     35  CB  ALA     5      28.136   8.252  30.019  1.00 17.83      1SRN 133
+ATOM     36  N   ALA     6      27.347   8.474  27.100  1.00 17.91      1SRN 134
+ATOM     37  CA  ALA     6      27.667   8.723  25.675  1.00 17.62      1SRN 135
+ATOM     38  C   ALA     6      26.563   9.530  25.053  1.00 17.34      1SRN 136
+ATOM     39  O   ALA     6      26.910  10.405  24.191  1.00 18.24      1SRN 137
+ATOM     40  CB  ALA     6      28.009   7.493  24.904  1.00 17.09      1SRN 138
+ATOM     41  N   LYS     7      25.331   9.253  25.468  1.00 16.74      1SRN 139
+ATOM     42  CA  LYS     7      24.214  10.046  24.882  1.00 15.77      1SRN 140
+ATOM     43  C   LYS     7      24.248  11.484  25.368  1.00 14.54      1SRN 141
+ATOM     44  O   LYS     7      23.864  12.449  24.637  1.00 14.65      1SRN 142
+ATOM     45  CB  LYS     7      22.873   9.453  25.223  1.00 15.88      1SRN 143
+ATOM     46  CG  LYS     7      21.741   9.892  24.304  1.00 16.30      1SRN 144
+ATOM     47  CD  LYS     7      20.430   9.673  25.048  1.00 15.98      1SRN 145
+ATOM     48  CE  LYS     7      19.195   9.601  24.179  1.00 17.66      1SRN 146
+ATOM     49  NZ  LYS     7      18.362   8.506  24.926  1.00 18.08      1SRN 147
+ATOM     50  N   PHE     8      24.611  11.716  26.577  1.00 12.90      1SRN 148
+ATOM     51  CA  PHE     8      24.684  13.122  27.093  1.00 11.39      1SRN 149
+ATOM     52  C   PHE     8      25.642  13.925  26.270  1.00 11.71      1SRN 150
+ATOM     53  O   PHE     8      25.432  15.007  25.725  1.00 11.29      1SRN 151
+ATOM     54  CB  PHE     8      25.131  13.060  28.561  1.00  9.51      1SRN 152
+ATOM     55  CG  PHE     8      25.203  14.394  29.198  1.00  8.62      1SRN 153
+ATOM     56  CD1 PHE     8      24.126  14.986  29.804  1.00  7.91      1SRN 154
+ATOM     57  CD2 PHE     8      26.452  15.039  29.163  1.00  7.74      1SRN 155
+ATOM     58  CE1 PHE     8      24.280  16.270  30.378  1.00  8.08      1SRN 156
+ATOM     59  CE2 PHE     8      26.616  16.300  29.751  1.00  7.25      1SRN 157
+ATOM     60  CZ  PHE     8      25.504  16.901  30.351  1.00  6.96      1SRN 158
+ATOM     61  N   GLU     9      26.898  13.337  26.165  1.00 11.99      1SRN 159
+ATOM     62  CA  GLU     9      27.881  14.091  25.359  1.00 12.32      1SRN 160
+ATOM     63  C   GLU     9      27.371  14.464  24.013  1.00 12.06      1SRN 161
+ATOM     64  O   GLU     9      27.476  15.538  23.451  1.00 12.44      1SRN 162
+ATOM     65  CB  GLU     9      29.091  13.150  25.107  1.00 12.85      1SRN 163
+ATOM     66  CG  GLU     9      30.026  13.107  26.317  1.00 15.11      1SRN 164
+ATOM     67  CD  GLU     9      30.913  11.894  26.266  1.00 15.07      1SRN 165
+ATOM     68  OE1 GLU     9      31.790  11.714  27.007  1.00 16.73      1SRN 166
+ATOM     69  OE2 GLU     9      30.618  11.126  25.332  1.00 15.20      1SRN 167
+ATOM     70  N   ARG    10      26.718  13.468  23.337  1.00 12.46      1SRN 168
+ATOM     71  CA  ARG    10      26.217  13.615  22.008  1.00 12.35      1SRN 169
+ATOM     72  C   ARG    10      25.181  14.741  21.898  1.00 12.46      1SRN 170
+ATOM     73  O   ARG    10      25.315  15.571  20.989  1.00 11.22      1SRN 171
+ATOM     74  CB  ARG    10      25.543  12.364  21.390  1.00 12.36      1SRN 172
+ATOM     75  CG  ARG    10      25.041  12.649  20.020  1.00 13.12      1SRN 173
+ATOM     76  CD  ARG    10      24.583  11.429  19.284  1.00 13.43      1SRN 174
+ATOM     77  NE  ARG    10      23.705  10.574  20.090  1.00 13.83      1SRN 175
+ATOM     78  CZ  ARG    10      22.391  10.715  20.025  1.00 13.92      1SRN 176
+ATOM     79  NH1 ARG    10      21.597   9.973  20.783  1.00 14.58      1SRN 177
+ATOM     80  NH2 ARG    10      21.916  11.570  19.124  1.00 14.10      1SRN 178
+ATOM     81  N   GLN    11      24.193  14.618  22.850  1.00 12.41      1SRN 179
+ATOM     82  CA  GLN    11      23.137  15.655  22.818  1.00 12.90      1SRN 180
+ATOM     83  C   GLN    11      23.542  16.942  23.484  1.00 12.41      1SRN 181
+ATOM     84  O   GLN    11      22.862  17.924  23.011  1.00 11.85      1SRN 182
+ATOM     85  CB  GLN    11      21.763  15.296  23.391  1.00 13.65      1SRN 183
+ATOM     86  CG  GLN    11      21.537  13.847  23.729  1.00 16.01      1SRN 184
+ATOM     87  CD  GLN    11      20.051  13.594  24.035  1.00 16.63      1SRN 185
+ATOM     88  OE1 GLN    11      19.210  13.643  23.132  1.00 17.16      1SRN 186
+ATOM     89  NE2 GLN    11      19.779  13.299  25.295  1.00 17.48      1SRN 187
+ATOM     90  N   HIS    12      24.459  17.136  24.385  1.00 12.05      1SRN 188
+ATOM     91  CA  HIS    12      24.725  18.429  24.940  1.00 12.48      1SRN 189
+ATOM     92  C   HIS    12      26.072  19.049  24.947  1.00 12.89      1SRN 190
+ATOM     93  O   HIS    12      26.138  20.232  25.394  1.00 12.54      1SRN 191
+ATOM     94  CB  HIS    12      24.368  18.383  26.521  1.00 13.26      1SRN 192
+ATOM     95  CG  HIS    12      22.979  17.885  26.681  1.00 13.16      1SRN 193
+ATOM     96  ND1 HIS    12      21.845  18.552  26.268  1.00 13.77      1SRN 194
+ATOM     97  CD2 HIS    12      22.549  16.744  27.261  1.00 13.98      1SRN 195
+ATOM     98  CE1 HIS    12      20.780  17.885  26.588  1.00 14.16      1SRN 196
+ATOM     99  NE2 HIS    12      21.188  16.738  27.201  1.00 14.44      1SRN 197
+ATOM    100  N   MET    13      27.098  18.382  24.448  1.00 13.80      1SRN 198
+ATOM    101  CA  MET    13      28.468  18.994  24.490  1.00 14.19      1SRN 199
+ATOM    102  C   MET    13      28.829  19.578  23.143  1.00 15.23      1SRN 200
+ATOM    103  O   MET    13      28.604  18.999  22.059  1.00 15.11      1SRN 201
+ATOM    104  CB  MET    13      29.418  17.918  24.907  1.00 14.55      1SRN 202
+ATOM    105  CG  MET    13      29.453  17.361  26.285  1.00 14.22      1SRN 203
+ATOM    106  SD  MET    13      29.520  18.746  27.500  1.00 13.21      1SRN 204
+ATOM    107  CE  MET    13      31.108  19.501  27.016  1.00 12.96      1SRN 205
+ATOM    108  O   MET    13      29.395  20.806  23.182  1.00 16.24      1SRN 206
+END
+
+
+
+
+

GROMACS/gmxdemo/em.mdp

+title               =  cpeptide
+cpp                 =  /usr/bin/cpp
+define              =  -DFLEX_SPC
+constraints         =  none
+integrator          =  steep
+nsteps              =  100
+nstlist             =  10
+ns_type             =  grid
+rlist               =  1.0
+rcoulomb            =  1.0
+rvdw                =  1.0
+;
+;       Energy minimizing stuff
+;
+emtol               =  1000.0
+emstep              =  0.01

GROMACS/gmxdemo/md.mdp

+title               =  cpeptide MD
+cpp                 =  /usr/bin/cpp
+constraints         =  all-bonds
+integrator          =  md
+dt                  =  0.002	; ps !
+nsteps              =  5000	; total 10.0 ps.
+nstcomm             =  1
+nstxout             =  50
+nstvout             =  0
+nstfout             =  0
+nstlist             =  10
+ns_type             =  grid
+rlist               =  1.0
+rcoulomb            =  1.0
+rvdw                =  1.0
+; Berendsen temperature coupling is on in two groups
+Tcoupl              =  berendsen
+tau_t               =  0.1	     0.1
+tc-grps		    =  protein	     sol
+ref_t               =  300	     300
+; Pressure coupling is not on
+Pcoupl              =  no
+tau_p               =  0.5
+compressibility     =  4.5e-5
+ref_p               =  1.0
+; Generate velocites is on at 300 K.
+gen_vel             =  yes
+gen_temp            =  300.0
+gen_seed            =  173529

GROMACS/gmxdemo/output.genbox

+editconf: Command not found.
+genbox: Command not found.

GROMACS/gmxdemo/output.grompp_em

+grompp: Command not found.

GROMACS/gmxdemo/output.grompp_md

+grompp: Command not found.

GROMACS/gmxdemo/output.grompp_pr

+grompp: Command not found.

GROMACS/gmxdemo/output.mdrun_em

+mdrun: Command not found.

GROMACS/gmxdemo/output.mdrun_md

+mdrun: Command not found.

GROMACS/gmxdemo/output.mdrun_pr

+mdrun: Command not found.

GROMACS/gmxdemo/output.pdb2gmx

+pdb2gmx: Command not found.

GROMACS/gmxdemo/pr.mdp

+title               =  cpeptide position restraining
+cpp                 =  /usr/bin/cpp
+define              =  -DPOSRES
+constraints         =  all-bonds
+integrator          =  md
+dt                  =  0.002	; ps !
+nsteps              =  500	; total 1.0 ps.
+nstcomm             =  1
+nstxout             =  10
+nstvout             =  1000
+nstfout             =  0
+nstlog              =  10
+nstenergy           =  10
+nstlist             =  10
+ns_type             =  grid
+rlist               =  1.0
+rcoulomb            =  1.0
+rvdw                =  1.0
+; Berendsen temperature coupling is on in two groups
+Tcoupl              =  berendsen
+tau_t               =  0.1      	0.1
+tc-grps		    =  protein  	sol
+ref_t               =  300      	300
+; Pressure coupling is not on
+Pcoupl              =  no
+tau_p               =  0.5
+compressibility     =  4.5e-5
+ref_p               =  1.0
+; Generate velocites is on at 300 K.
+gen_vel             =  yes
+gen_temp            =  300.0
+gen_seed            =  173529

GROMACS/methanol/grompp.mdp

+;
+;	File 'mdout.mdp' was generated
+;	By user: spoel (291)
+;	On host: chagall
+;	At date: Mon Dec 15 13:52:23 2003
+;
+
+; VARIOUS PREPROCESSING OPTIONS
+title                    = Yo
+cpp                      = /usr/bin/cpp
+include                  = 
+define                   = 
+
+; RUN CONTROL PARAMETERS
+integrator               = md
+; Start time and timestep in ps
+tinit                    = 0
+dt                       = 0.002
+nsteps                   = 10000
+; For exact run continuation or redoing part of a run
+init_step                = 0
+; mode for center of mass motion removal
+comm-mode                = Linear
+; number of steps for center of mass motion removal
+nstcomm                  = 1
+; group(s) for center of mass motion removal
+comm-grps                = 
+
+; LANGEVIN DYNAMICS OPTIONS
+; Temperature, friction coefficient (amu/ps) and random seed
+bd-temp                  = 300
+bd-fric                  = 0
+ld-seed                  = 1993
+
+; ENERGY MINIMIZATION OPTIONS
+; Force tolerance and initial step-size
+emtol                    = 100
+emstep                   = 0.01
+; Max number of iterations in relax_shells
+niter                    = 20
+; Step size (1/ps^2) for minimization of flexible constraints
+fcstep                   = 0
+; Frequency of steepest descents steps when doing CG
+nstcgsteep               = 1000
+nbfgscorr                = 10
+
+; OUTPUT CONTROL OPTIONS
+; Output frequency for coords (x), velocities (v) and forces (f)
+nstxout                  = 0
+nstvout                  = 0
+nstfout                  = 0
+; Checkpointing helps you continue after crashes
+nstcheckpoint            = 1000
+; Output frequency for energies to log file and energy file
+nstlog                   = 50
+nstenergy                = 50
+; Output frequency and precision for xtc file
+nstxtcout                = 50
+xtc-precision            = 1000
+; This selects the subset of atoms for the xtc file. You can
+; select multiple groups. By default all atoms will be written.
+xtc-grps                 = 
+; Selection of energy groups
+energygrps               = 
+
+; NEIGHBORSEARCHING PARAMETERS
+; nblist update frequency
+nstlist                  = 5
+; ns algorithm (simple or grid)
+ns_type                  = grid
+; Periodic boundary conditions: xyz (default), no (vacuum)
+; or full (infinite systems only)
+pbc                      = xyz
+; nblist cut-off        
+rlist                    = 0.9
+domain-decomposition     = no
+
+; OPTIONS FOR ELECTROSTATICS AND VDW
+; Method for doing electrostatics
+coulombtype              = Cut-off
+rcoulomb-switch          = 0
+rcoulomb                 = 0.9
+; Dielectric constant (DC) for cut-off or DC of reaction field
+epsilon-r                = 1
+; Method for doing Van der Waals
+vdw-type                 = Cut-off
+; cut-off lengths       
+rvdw-switch              = 0
+rvdw                     = 0.9
+; Apply long range dispersion corrections for Energy and Pressure
+DispCorr                 = EnerPres
+; Extension of the potential lookup tables beyond the cut-off
+table-extension          = 1
+; Spacing for the PME/PPPM FFT grid
+fourierspacing           = 0.12
+; FFT grid size, when a value is 0 fourierspacing will be used
+fourier_nx               = 0
+fourier_ny               = 0
+fourier_nz               = 0
+; EWALD/PME/PPPM parameters
+pme_order                = 4
+ewald_rtol               = 1e-05
+ewald_geometry           = 3d
+epsilon_surface          = 0
+optimize_fft             = no
+
+; GENERALIZED BORN ELECTROSTATICS
+; Algorithm for calculating Born radii
+gb_algorithm             = Still
+; Frequency of calculating the Born radii inside rlist
+nstgbradii               = 1
+; Cutoff for Born radii calculation; the contribution from atoms
+; between rlist and rgbradii is updated every nstlist steps
+rgbradii                 = 2
+; Salt concentration in M for Generalized Born models
+gb_saltconc              = 0
+
+; IMPLICIT SOLVENT (for use with Generalized Born electrostatics)
+implicit_solvent         = No
+
+; OPTIONS FOR WEAK COUPLING ALGORITHMS
+; Temperature coupling  
+Tcoupl                   = berendsen
+; Groups to couple separately
+tc-grps                  = System
+; Time constant (ps) and reference temperature (K)
+tau_t                    = 0.1
+ref_t                    = 300
+; Pressure coupling     
+Pcoupl                   = berendsen
+Pcoupltype               = isotropic
+; Time constant (ps), compressibility (1/bar) and reference P (bar)
+tau_p                    = 1.0
+compressibility          = 4.5e-5
+ref_p                    = 1.0
+; Random seed for Andersen thermostat
+andersen_seed            = 815131
+
+; SIMULATED ANNEALING  
+; Type of annealing for each temperature group (no/single/periodic)
+annealing                = no
+; Number of time points to use for specifying annealing in each group
+annealing_npoints        = 
+; List of times at the annealing points for each group
+annealing_time           = 
+; Temp. at each annealing point, for each group.
+annealing_temp           = 
+
+; GENERATE VELOCITIES FOR STARTUP RUN
+gen_vel                  = yes
+gen_temp                 = 300
+gen_seed                 = 1993
+
+; OPTIONS FOR BONDS    
+constraints              = all-bonds
+; Type of constraint algorithm
+constraint-algorithm     = Lincs
+; Do not constrain the start configuration
+unconstrained-start      = no
+; Use successive overrelaxation to reduce the number of shake iterations
+Shake-SOR                = no
+; Relative tolerance of shake
+shake-tol                = 1e-04
+; Highest order in the expansion of the constraint coupling matrix
+lincs-order              = 4
+; Number of iterations in the final step of LINCS. 1 is fine for
+; normal simulations, but use 2 to conserve energy in NVE runs.
+; For energy minimization with constraints it should be 4 to 8.
+lincs-iter               = 1
+; Lincs will write a warning to the stderr if in one step a bond
+; rotates over more degrees than
+lincs-warnangle          = 30
+; Convert harmonic bonds to morse potentials
+morse                    = no
+
+; ENERGY GROUP EXCLUSIONS
+; Pairs of energy groups for which all non-bonded interactions are excluded
+energygrp_excl           = 
+
+; NMR refinement stuff 
+; Distance restraints type: No, Simple or Ensemble
+disre                    = No
+; Force weighting of pairs in one distance restraint: Conservative or Equal
+disre-weighting          = Conservative
+; Use sqrt of the time averaged times the instantaneous violation
+disre-mixed              = no
+disre-fc                 = 1000
+disre-tau                = 0
+; Output frequency for pair distances to energy file
+nstdisreout              = 100
+; Orientation restraints: No or Yes
+orire                    = no
+; Orientation restraints force constant and tau for time averaging
+orire-fc                 = 0
+orire-tau                = 0
+orire-fitgrp             = 
+; Output frequency for trace(SD) to energy file
+nstorireout              = 100
+; Dihedral angle restraints: No, Simple or Ensemble
+dihre                    = No
+dihre-fc                 = 1000
+dihre-tau                = 0
+; Output frequency for dihedral values to energy file
+nstdihreout              = 100
+
+; Free energy control stuff
+free-energy              = no
+init-lambda              = 0
+delta-lambda             = 0
+sc-alpha                 = 0
+sc-sigma                 = 0.3
+
+; Non-equilibrium MD stuff
+acc-grps                 = 
+accelerate               = 
+freezegrps               = 
+freezedim                = 
+cos-acceleration         = 0
+
+; Electric fields      
+; Format is number of terms (int) and for all terms an amplitude (real)
+; and a phase angle (real)
+E-x                      = 
+E-xt                     = 
+E-y                      = 
+E-yt                     = 
+E-z                      = 
+E-zt                     = 
+
+; User defined thingies
+user1-grps               = 
+user2-grps               = 
+userint1                 = 0
+userint2                 = 0
+userint3                 = 0
+userint4                 = 0
+userreal1                = 0
+userreal2                = 0
+userreal3                = 0
+userreal4                = 0

GROMACS/methanol/index.ndx

+[ MeOH ]
+   1    2    3    4    5    6    7    8    9   10   11   12   13   14   15 
+  16   17   18   19   20   21   22   23   24   25   26   27   28   29   30 
+  31   32   33   34   35   36   37   38   39   40   41   42   43   44   45 
+  46   47   48   49   50   51   52   53   54   55   56   57   58   59   60 
+  61   62   63   64   65   66   67   68   69   70   71   72   73   74   75 
+  76   77   78   79   80   81   82   83   84   85   86   87   88   89   90 
+  91   92   93   94   95   96   97   98   99  100  101  102  103  104  105 
+ 106  107  108  109  110  111  112  113  114  115  116  117  118  119  120 
+ 121  122  123  124  125  126  127  128  129  130  131  132  133  134  135 
+ 136  137  138  139  140  141  142  143  144  145  146  147  148  149  150 
+ 151  152  153  154  155  156  157  158  159  160  161  162  163  164  165 
+ 166  167  168  169  170  171  172  173  174  175  176  177  178  179  180 
+ 181  182  183  184  185  186  187  188  189  190  191  192  193  194  195 
+ 196  197  198  199  200  201  202  203  204  205  206  207  208  209  210 
+ 211  212  213  214  215  216  217  218  219  220  221  222  223  224  225 
+ 226  227  228  229  230  231  232  233  234  235  236  237  238  239  240 
+ 241  242  243  244  245  246  247  248  249  250  251  252  253  254  255 
+ 256  257  258  259  260  261  262  263  264  265  266  267  268  269  270 
+ 271  272  273  274  275  276  277  278  279  280  281  282  283  284  285 
+ 286  287  288  289  290  291  292  293  294  295  296  297  298  299  300 
+ 301  302  303  304  305  306  307  308  309  310  311  312  313  314  315 
+ 316  317  318  319  320  321  322  323  324  325  326  327  328  329  330 
+ 331  332  333  334  335  336  337  338  339  340  341  342  343  344  345 
+ 346  347  348  349  350  351  352  353  354  355  356  357  358  359  360 
+ 361  362  363  364  365  366  367  368  369  370  371  372  373  374  375 
+ 376  377  378  379  380  381  382  383  384  385  386  387  388  389  390 
+ 391  392  393  394  395  396  397  398  399  400  401  402  403  404  405 
+ 406  407  408  409  410  411  412  413  414  415  416  417  418  419  420 
+ 421  422  423  424  425  426  427  428  429  430  431  432  433  434  435 
+ 436  437  438  439  440  441  442  443  444  445  446  447  448  449  450 
+ 451  452  453  454  455  456  457  458  459  460  461  462  463  464  465 
+ 466  467  468  469  470  471  472  473  474  475  476  477  478  479  480 
+ 481  482  483  484  485  486  487  488  489  490  491  492  493  494  495 
+ 496  497  498  499  500  501  502  503  504  505  506  507  508  509  510 
+ 511  512  513  514  515  516  517  518  519  520  521  522  523  524  525 
+ 526  527  528  529  530  531  532  533  534  535  536  537  538  539  540 
+ 541  542  543  544  545  546  547  548  549  550  551  552  553  554  555 
+ 556  557  558  559  560  561  562  563  564  565  566  567  568  569  570 
+ 571  572  573  574  575  576  577  578  579  580  581  582  583  584  585 
+ 586  587  588  589  590  591  592  593  594  595  596  597  598  599  600 
+ 601  602  603  604  605  606  607  608  609  610  611  612  613  614  615 
+ 616  617  618  619  620  621  622  623  624  625  626  627  628  629  630 
+ 631  632  633  634  635  636  637  638  639  640  641  642  643  644  645 
+ 646  647  648 
+[ ME1 ]
+   1    4    7   10   13   16   19   22   25   28   31   34   37   40   43 
+  46   49   52   55   58   61   64   67   70   73   76   79   82   85   88 
+  91   94   97  100  103  106  109  112  115  118  121  124  127  130  133 
+ 136  139  142  145  148  151  154  157  160  163  166  169  172  175  178 
+ 181  184  187  190  193  196  199  202  205  208  211  214  217  220  223 
+ 226  229  232  235  238  241  244  247  250  253  256  259  262  265  268 
+ 271  274  277  280  283  286  289  292  295  298  301  304  307  310  313 
+ 316  319  322  325  328  331  334  337  340  343  346  349  352  355  358 
+ 361  364  367  370  373  376  379  382  385  388  391  394  397  400  403 
+ 406  409  412  415  418  421  424  427  430  433  436  439  442  445  448 
+ 451  454  457  460  463  466  469  472  475  478  481  484  487  490  493 
+ 496  499  502  505  508  511  514  517  520  523  526  529  532  535  538 
+ 541  544  547  550  553  556  559  562  565  568  571  574  577  580  583 
+ 586  589  592  595  598  601  604  607  610  613  616  619  622  625  628 
+ 631  634  637  640  643  646 
+[ O2 ]
+   2    5    8   11   14   17   20   23   26   29   32   35   38   41   44 
+  47   50   53   56   59   62   65   68   71   74   77   80   83   86   89 
+  92   95   98  101  104  107  110  113  116  119  122  125  128  131  134 
+ 137  140  143  146  149  152  155  158  161  164  167  170  173  176  179 
+ 182  185  188  191  194  197  200  203  206  209  212  215  218  221  224 
+ 227  230  233  236  239  242  245  248  251  254  257  260  263  266  269 
+ 272  275  278  281  284  287  290  293  296  299  302  305  308  311  314 
+ 317  320  323  326  329  332  335  338  341  344  347  350  353  356  359 
+ 362  365  368  371  374  377  380  383  386  389  392  395  398  401  404 
+ 407  410  413  416  419  422  425  428  431  434  437  440  443  446  449 
+ 452  455  458  461  464  467  470  473  476  479  482  485  488  491  494 
+ 497  500  503  506  509  512  515  518  521  524  527  530  533  536  539 
+ 542  545  548  551  554  557  560  563  566  569  572  575  578  581  584 
+ 587  590  593  596  599  602  605  608  611  614  617  620  623  626  629 
+ 632  635  638  641  644  647 

GROMACS/methanol/methanol.itp

+#ifndef _FF_GROMOS96
+
+[ atomtypes ]
+;   type      mass    charge    ptype       c6            c12
+    OMet    15.999    -0.69     A	2.6169e-3      2.5231e-6
+      OW    15.999    -0.82     A	2.6170e-3      2.6330e-6
+    CMet    15.035     0.29     A	8.8758e-3     17.8426e-6
+       H     1.008     0.4      A	0.0            0.0
+      HW     1.008     0.41     A	0.0            0.0
+#endif
+
+[ moleculetype ]
+; name  nrexcl
+Methanol        2
+
+[ atoms ]
+;   nr  type    resnr   residu  atom    cgnr    charge	mass
+#ifdef _FF_GROMOS96
+1       CMet     1       MeOH    Me1     1        0.176 15.035   
+2       OMet     1       MeOH    O2      1       -0.574 15.999 
+3       H        1       MeOH    H3      1        0.398  1.008 
+#else
+1       CMet     1       MeOH    Me1     1        0.29  15.035
+2       OMet     1       MeOH    O2      1       -0.69  15.999
+3       H        1       MeOH    H3      1        0.40   1.008
+#endif
+
+[ bonds ]
+;  ai  aj funct           c0           c1
+1       2	1	   0.13600     376560.
+2       3	1	   0.10000     313800.
+
+[ angles ]
+;  ai    aj    ak       funct   c0      c1
+    1     2     3       1       108.53  397.5
+

GROMACS/methanol/topol.top

+#include "gromos43a1.ff/forcefield.itp"
+#include "methanol.itp"
+
+[ system ]
+Pure Methanol - Yummie!
+
+[ molecules ]
+Methanol	216
+

GROMACS/mixed/grompp.mdp

+;
+;	File 'mdout.mdp' was generated
+;	By user: spoel (291)
+;	On host: chagall
+;	At date: Mon Dec 15 13:53:04 2003
+;
+
+; VARIOUS PREPROCESSING OPTIONS
+title                    = Yo
+cpp                      = /usr/bin/cpp
+include                  = 
+define                   = 
+
+; RUN CONTROL PARAMETERS
+integrator               = md
+; Start time and timestep in ps
+tinit                    = 0
+dt                       = 0.002
+nsteps                   = 500000
+; For exact run continuation or redoing part of a run
+init_step                = 0
+; mode for center of mass motion removal
+comm-mode                = Linear
+; number of steps for center of mass motion removal
+nstcomm                  = 1
+; group(s) for center of mass motion removal
+comm-grps                = 
+
+; LANGEVIN DYNAMICS OPTIONS
+; Temperature, friction coefficient (amu/ps) and random seed
+bd-temp                  = 300
+bd-fric                  = 0
+ld-seed                  = 1993
+
+; ENERGY MINIMIZATION OPTIONS
+; Force tolerance and initial step-size
+emtol                    = 100
+emstep                   = 0.01
+; Max number of iterations in relax_shells
+niter                    = 20
+; Step size (1/ps^2) for minimization of flexible constraints
+fcstep                   = 0
+; Frequency of steepest descents steps when doing CG
+nstcgsteep               = 1000
+nbfgscorr                = 10
+
+; OUTPUT CONTROL OPTIONS
+; Output frequency for coords (x), velocities (v) and forces (f)
+nstxout                  = 0
+nstvout                  = 0
+nstfout                  = 0
+; Checkpointing helps you continue after crashes
+nstcheckpoint            = 1000
+; Output frequency for energies to log file and energy file
+nstlog                   = 250
+nstenergy                = 50
+; Output frequency and precision for xtc file
+nstxtcout                = 250
+xtc-precision            = 1000
+; This selects the subset of atoms for the xtc file. You can
+; select multiple groups. By default all atoms will be written.
+xtc-grps                 = 
+; Selection of energy groups
+energygrps               = 
+
+; NEIGHBORSEARCHING PARAMETERS
+; nblist update frequency
+nstlist                  = 5
+; ns algorithm (simple or grid)
+ns_type                  = grid
+; Periodic boundary conditions: xyz (default), no (vacuum)
+; or full (infinite systems only)
+pbc                      = xyz
+; nblist cut-off        
+rlist                    = 0.9
+domain-decomposition     = no
+
+; OPTIONS FOR ELECTROSTATICS AND VDW
+; Method for doing electrostatics
+coulombtype              = Cut-off
+rcoulomb-switch          = 0
+rcoulomb                 = 0.9
+; Dielectric constant (DC) for cut-off or DC of reaction field
+epsilon-r                = 1
+; Method for doing Van der Waals
+vdw-type                 = Cut-off
+; cut-off lengths       
+rvdw-switch              = 0
+rvdw                     = 0.9
+; Apply long range dispersion corrections for Energy and Pressure
+DispCorr                 = EnerPres
+; Extension of the potential lookup tables beyond the cut-off
+table-extension          = 1
+; Spacing for the PME/PPPM FFT grid
+fourierspacing           = 0.12
+; FFT grid size, when a value is 0 fourierspacing will be used
+fourier_nx               = 0
+fourier_ny               = 0
+fourier_nz               = 0
+; EWALD/PME/PPPM parameters
+pme_order                = 4
+ewald_rtol               = 1e-05
+ewald_geometry           = 3d
+epsilon_surface          = 0
+optimize_fft             = no
+
+; GENERALIZED BORN ELECTROSTATICS
+; Algorithm for calculating Born radii
+gb_algorithm             = Still
+; Frequency of calculating the Born radii inside rlist
+nstgbradii               = 1
+; Cutoff for Born radii calculation; the contribution from atoms
+; between rlist and rgbradii is updated every nstlist steps
+rgbradii                 = 2
+; Salt concentration in M for Generalized Born models
+gb_saltconc              = 0
+
+; IMPLICIT SOLVENT (for use with Generalized Born electrostatics)
+implicit_solvent         = No
+
+; OPTIONS FOR WEAK COUPLING ALGORITHMS
+; Temperature coupling  
+Tcoupl                   = berendsen
+; Groups to couple separately
+tc-grps                  = MeOH	SOL
+; Time constant (ps) and reference temperature (K)
+tau_t                    = 0.1	0.1
+ref_t                    = 300	300
+; Pressure coupling     
+Pcoupl                   = berendsen
+Pcoupltype               = anisotropic
+; Time constant (ps), compressibility (1/bar) and reference P (bar)
+tau_p                    = 2.0
+compressibility          = 5e-5 5e-5 5e-5 0 0 0
+ref_p                    = 1	1	1	0	0	0
+; Random seed for Andersen thermostat
+andersen_seed            = 815131
+
+; SIMULATED ANNEALING  
+; Type of annealing for each temperature group (no/single/periodic)
+annealing                = no no
+; Number of time points to use for specifying annealing in each group
+annealing_npoints        = 
+; List of times at the annealing points for each group
+annealing_time           = 
+; Temp. at each annealing point, for each group.
+annealing_temp           = 
+
+; GENERATE VELOCITIES FOR STARTUP RUN
+gen_vel                  = yes
+gen_temp                 = 300
+gen_seed                 = 1993
+
+; OPTIONS FOR BONDS    
+constraints              = all-bonds
+; Type of constraint algorithm
+constraint-algorithm     = Lincs
+; Do not constrain the start configuration
+unconstrained-start      = no
+; Use successive overrelaxation to reduce the number of shake iterations
+Shake-SOR                = no
+; Relative tolerance of shake
+shake-tol                = 1e-04
+; Highest order in the expansion of the constraint coupling matrix
+lincs-order              = 4
+; Number of iterations in the final step of LINCS. 1 is fine for
+; normal simulations, but use 2 to conserve energy in NVE runs.
+; For energy minimization with constraints it should be 4 to 8.
+lincs-iter               = 1
+; Lincs will write a warning to the stderr if in one step a bond
+; rotates over more degrees than
+lincs-warnangle          = 30
+; Convert harmonic bonds to morse potentials
+morse                    = no
+
+; ENERGY GROUP EXCLUSIONS
+; Pairs of energy groups for which all non-bonded interactions are excluded
+energygrp_excl           = 
+
+; NMR refinement stuff 
+; Distance restraints type: No, Simple or Ensemble
+disre                    = No
+; Force weighting of pairs in one distance restraint: Conservative or Equal
+disre-weighting          = Conservative
+; Use sqrt of the time averaged times the instantaneous violation
+disre-mixed              = no
+disre-fc                 = 1000
+disre-tau                = 0
+; Output frequency for pair distances to energy file
+nstdisreout              = 100
+; Orientation restraints: No or Yes
+orire                    = no
+; Orientation restraints force constant and tau for time averaging
+orire-fc                 = 0
+orire-tau                = 0
+orire-fitgrp             = 
+; Output frequency for trace(SD) to energy file
+nstorireout              = 100
+; Dihedral angle restraints: No, Simple or Ensemble
+dihre                    = No
+dihre-fc                 = 1000
+dihre-tau                = 0
+; Output frequency for dihedral values to energy file
+nstdihreout              = 100
+
+; Free energy control stuff
+free-energy              = no
+init-lambda              = 0
+delta-lambda             = 0
+sc-alpha                 = 0
+sc-sigma                 = 0.3
+
+; Non-equilibrium MD stuff
+acc-grps                 = 
+accelerate               = 
+freezegrps               = 
+freezedim                = 
+cos-acceleration         = 0
+
+; Electric fields      
+; Format is number of terms (int) and for all terms an amplitude (real)
+; and a phase angle (real)
+E-x                      = 
+E-xt                     = 
+E-y                      = 
+E-yt                     = 
+E-z                      = 
+E-zt                     = 
+
+; User defined thingies
+user1-grps               = 
+user2-grps               = 
+userint1                 = 0
+userint2                 = 0
+userint3                 = 0
+userint4                 = 0
+userreal1                = 0
+userreal2                = 0
+userreal3                = 0
+userreal4                = 0

GROMACS/mixed/topol.top

+#include "gromos43a1.ff/forcefield.itp"
+#include "methanol.itp"
+#include "spc.itp"
+
+[ system ]
+Pure Methanol - Yummie! (and some water)
+
+[ molecules ]
+Methanol	216
+SOL		216

GROMACS/nmr1/conf.gro

+"Check Your Input" (D. van der Spoel)
+   59
+    1TYR      N    1   1.521   1.583   2.009  0.0000  0.0000  0.0000
+    1TYR     H1    2   1.421   1.595   2.009  0.0000  0.0000  0.0000
+    1TYR     H2    3   1.548   1.533   1.927  0.0000  0.0000  0.0000
+    1TYR     CA    4   1.585   1.713   2.009  0.0000  0.0000  0.0000
+    1TYR     HA    5   1.555   1.760   1.926  0.0000  0.0000  0.0000
+    1TYR     CB    6   1.541   1.791   2.133  0.0000  0.0000  0.0000
+    1TYR    HB1    7   1.479   1.735   2.187  0.0000  0.0000  0.0000
+    1TYR    HB2    8   1.622   1.813   2.188  0.0000  0.0000  0.0000
+    1TYR     CG    9   1.472   1.919   2.098  0.0000  0.0000  0.0000
+    1TYR    CD1   10   1.335   1.925   2.079  0.0000  0.0000  0.0000
+    1TYR    HD1   11   1.279   1.843   2.090  0.0000  0.0000  0.0000
+    1TYR    CD2   12   1.541   2.038   2.081  0.0000  0.0000  0.0000
+    1TYR    HD2   13   1.640   2.040   2.093  0.0000  0.0000  0.0000
+    1TYR    CE1   14   1.275   2.045   2.046  0.0000  0.0000  0.0000
+    1TYR    HE1   15   1.177   2.028   2.038  0.0000  0.0000  0.0000
+    1TYR    CE2   16   1.472   2.153   2.047  0.0000  0.0000  0.0000
+    1TYR    HE2   17   1.544   2.222   2.042  0.0000  0.0000  0.0000
+    1TYR     CZ   18   1.352   2.159   2.031  0.0000  0.0000  0.0000
+    1TYR     OH   19   1.306   2.253   2.005  0.0000  0.0000  0.0000
+    1TYR     HH   20   1.291   2.349   1.983  0.0000  0.0000  0.0000
+    1TYR      C   21   1.737   1.695   2.009  0.0000  0.0000  0.0000
+    1TYR      O   22   1.789   1.585   2.009  0.0000  0.0000  0.0000
+    2ALA      N   23   1.803   1.813   2.009  0.0000  0.0000  0.0000
+    2ALA      H   24   1.755   1.900   2.009  0.0000  0.0000  0.0000
+    2ALA     CA   25   1.949   1.808   2.009  0.0000  0.0000  0.0000
+    2ALA     HA   26   1.976   1.761   2.093  0.0000  0.0000  0.0000
+    2ALA     CB   27   1.994   1.731   1.885  0.0000  0.0000  0.0000
+    2ALA    HB1   28   2.094   1.726   1.882  0.0000  0.0000  0.0000
+    2ALA    HB2   29   1.956   1.638   1.887  0.0000  0.0000  0.0000
+    2ALA    HB3   30   1.961   1.778   1.803  0.0000  0.0000  0.0000
+    2ALA      C   31   2.011   1.948   2.009  0.0000  0.0000  0.0000
+    2ALA      O   32   1.942   2.049   2.009  0.0000  0.0000  0.0000
+    3SER      N   33   2.145   1.946   2.009  0.0000  0.0000  0.0000
+    3SER      H   34   2.177   1.851   2.009  0.0000  0.0000  0.0000
+    3SER     CA   35   2.214   2.073   2.009  0.0000  0.0000  0.0000
+    3SER     HA   36   2.186   2.121   1.926  0.0000  0.0000  0.0000
+    3SER     CB   37   2.174   2.152   2.133  0.0000  0.0000  0.0000
+    3SER    HB1   38   2.076   2.170   2.134  0.0000  0.0000  0.0000
+    3SER    HB2   39   2.200   2.103   2.217  0.0000  0.0000  0.0000
+    3SER     OG   40   2.240   2.276   2.136  0.0000  0.0000  0.0000
+    3SER     HG   41   2.270   2.367   2.165  0.0000  0.0000  0.0000
+    3SER      C   42   2.365   2.049   2.009  0.0000  0.0000  0.0000
+    3SER      O   43   2.413   1.937   2.009  0.0000  0.0000  0.0000
+    4THR      N   44   2.437   2.163   2.009  0.0000  0.0000  0.0000
+    4THR      H   45   2.374   2.242   2.009  0.0000  0.0000  0.0000
+    4THR     CA   46   2.581   2.152   2.009  0.0000  0.0000  0.0000
+    4THR     HA   47   2.606   2.102   2.092  0.0000  0.0000  0.0000
+    4THR     CB   48   2.627   2.077   1.884  0.0000  0.0000  0.0000
+    4THR     HB   49   2.590   1.984   1.889  0.0000  0.0000  0.0000
+    4THR    OG1   50   2.767   2.065   1.882  0.0000  0.0000  0.0000
+    4THR    HG1   51   2.859   2.041   1.853  0.0000  0.0000  0.0000
+    4THR    CG2   52   2.585   2.146   1.754  0.0000  0.0000  0.0000
+    4THR   HG21   53   2.617   2.093   1.676  0.0000  0.0000  0.0000
+    4THR   HG22   54   2.485   2.154   1.751  0.0000  0.0000  0.0000
+    4THR   HG23   55   2.625   2.238   1.751  0.0000  0.0000  0.0000
+    4THR      C   56   2.643   2.292   2.009  0.0000  0.0000  0.0000
+    4THR     OT   57   2.709   2.368   2.009  0.0000  0.0000  0.0000
+    4THR      O   58   2.574   2.394   2.009  0.0000  0.0000  0.0000
+    4THR     HO   59   2.543   2.489   2.009  0.0000  0.0000  0.0000
+   4.00000   4.00000   4.00000   0.00000   0.00000   0.00000   0.00000   0.00000   0.00000

GROMACS/nmr1/grompp.mdp

+
+; VARIOUS PREPROCESSING OPTIONS = 
+title                    = Yo
+cpp                      = /usr/bin/cpp
+include                  = -I../top
+define                   = 
+
+; RUN CONTROL PARAMETERS = 
+integrator               = md
+; start time and timestep in ps = 
+tinit                    = 0.0
+dt                       = 0.002
+nsteps                   = 5000
+; number of steps for center of mass motion removal = 
+nstcomm                  = 1
+comm-grps                =
+
+; LANGEVIN DYNAMICS OPTIONS = 
+; Temperature, friction coefficient (amu/ps) and random seed = 
+bd-temp                  = 300
+bd-fric                  = 0
+ld-seed                  = 1993
+
+; ENERGY MINIMIZATION OPTIONS = 
+; Force tolerance and initial step-size = 
+emtol                    = 0.001
+emstep                   = 0.1
+; Max number of iterations in relax_shells = 
+niter                    = 0
+; Frequency of steepest descents steps when doing CG = 
+nstcgsteep               = 1000
+
+; OUTPUT CONTROL OPTIONS = 
+; Output frequency for coords (x), velocities (v) and forces (f) = 
+nstxout                  = 10
+nstvout                  = 0
+nstfout                  = 0
+; Output frequency for energies to log file and energy file = 
+nstlog                   = 100
+nstenergy                = 100
+; Output frequency and precision for xtc file = 
+nstxtcout                = 10
+xtc_precision            = 1000
+; This selects the subset of atoms for the xtc file. You can = 
+; select multiple groups. By default all atoms will be written. = 
+xtc-grps                 = 
+; Selection of energy groups = 
+energygrps               = System
+
+; NEIGHBORSEARCHING PARAMETERS = 
+; nblist update frequency = 
+nstlist                  = 100
+; ns algorithm (simple or grid) = 
+ns_type                  = simple
+; Periodic boundary conditions: xyz or none = 
+pbc                      = xyz
+; nblist cut-off         = 
+rlist                    = 1
+domain-decomposition     = no
+
+; OPTIONS FOR ELECTROSTATICS AND VDW = 
+; Method for doing electrostatics = 
+coulombtype              = Cut-off
+rcoulomb-switch          = 0
+rcoulomb                 = 1
+; Dielectric constant (DC) for cut-off or DC of reaction field = 
+epsilon_r                = 1.0
+; Method for doing Van der Waals = 
+vdw-type                 = Cut-off
+; cut-off lengths        = 
+rvdw-switch              = 0
+rvdw                     = 1
+; Apply long range dispersion corrections for Energy and Pressure = 
+DispCorr                = no
+; Spacing for the PME/PPPM FFT grid = 
+fourierspacing           = 0.12
+; FFT grid size, when a value is 0 fourierspacing will be used = 
+fourier_nx               = 0
+fourier_ny               = 0
+fourier_nz               = 0
+; EWALD/PME/PPPM parameters = 
+pme_order                = 4
+ewald_rtol               = 1e-05
+epsilon_surface          = 0
+optimize_fft             = no
+
+; OPTIONS FOR WEAK COUPLING ALGORITHMS = 
+; Temperature coupling   = 
+tcoupl                   = berendsen
+; Groups to couple separately = 
+tc-grps                  = System
+; Time constant (ps) and reference temperature (K) = 
+tau_t                    = 0.1
+ref_t                    = 300
+; Pressure coupling      = 
+Pcoupl                   = no
+Pcoupltype               = Isotropic
+; Time constant (ps), compressibility (1/bar) and reference P (bar) = 
+tau_p                    = 1
+compressibility          = 
+ref_p                    = 1.0	1.0	1.0
+
+; SIMULATED ANNEALING CONTROL = 
+annealing                = no
+; Time at which temperature should be zero (ps) = 
+zero-temp_time           = 0
+
+; GENERATE VELOCITIES FOR STARTUP RUN = 
+gen_vel                  = yes
+gen_temp                 = 300.0
+gen_seed                 = 173529
+
+; OPTIMIZATIONS FOR SOLVENT MODELS = 
+; Solvent molecule name (blank: no optimization) = 
+solvent-optimization     = 
+
+; OPTIONS FOR BONDS     = 
+constraints              = none
+; Type of constraint algorithm = 
+constraint-algorithm     = Lincs
+; Do not constrain the start configuration = 
+unconstrained-start      = no
+; Relative tolerance of shake = 
+shake-tol                = 1e-04
+; Highest order in the expansion of the constraint coupling matrix = 
+lincs-order              = 4
+; Lincs will write a warning to the stderr if in one step a bond = 
+; rotates over more degrees than = 
+lincs-warnangle          = 30
+; Convert harmonic bonds to morse potentials = 
+morse                    = no
+
+; NMR refinement stuff  = 
+; Distance restraints type: No, Simple or Ensemble = 
+disre                    = Simple
+; Force weighting of pairs in one distance restraint: Equal or Conservative = 
+disre-weighting          = Equal
+; Use sqrt of the time averaged times the instantaneous violation = 
+disre-mixed              = no
+disre_fc                 = 1000
+disre_tau                = 0.0
+; Output frequency for pair distances to energy file = 
+nstdisreout              = 100
+
+; Free energy control stuff = 
+free-energy              = no
+init-lambda              = 0
+delta-lambda             = 0
+sc-alpha                 = 0
+sc-sigma                 = 0.3
+
+; Non-equilibrium MD stuff = 
+acc-grps                 = 
+accelerate               = 
+freezegrps               = 
+freezedim                = 
+cos-acceleration         = 0
+energygrp_excl           = 
+
+; Electric fields       = 
+; Format is number of terms (int) and for all terms an amplitude (real) = 
+; and a phase angle (real) = 
+E-x                      = 
+E-xt                     = 
+E-y                      = 
+E-yt                     = 
+E-z                      = 
+E-zt                     = 
+
+; User defined thingies = 
+user1-grps               = 
+user2-grps               = 
+userint1                 = 0
+userint2                 = 0
+userint3                 = 0
+userint4                 = 0
+userreal1                = 0
+userreal2                = 0
+userreal3                = 0
+userreal4                = 0

GROMACS/nmr1/pep.pdb

+ATOM      1  N   TYR     1      15.210  15.830  20.090  0.00  0.00
+ATOM      2  H1  TYR     1      14.210  15.950  20.090  0.00  0.00
+ATOM      3  H2  TYR     1      15.480  15.330  19.270  0.00  0.00
+ATOM      4  CA  TYR     1      15.850  17.130  20.090  0.00  0.00
+ATOM      5  HA  TYR     1      15.550  17.600  19.260  0.00  0.00
+ATOM      6  CB  TYR     1      15.410  17.910  21.330  0.00  0.00
+ATOM      7  HB1 TYR     1      14.790  17.350  21.870  0.00  0.00
+ATOM      8  HB2 TYR     1      16.220  18.130  21.880  0.00  0.00
+ATOM      9  CG  TYR     1      14.720  19.190  20.980  0.00  0.00
+ATOM     10  CD1 TYR     1      13.350  19.250  20.790  0.00  0.00
+ATOM     11  HD1 TYR     1      12.790  18.430  20.900  0.00  0.00
+ATOM     12  CD2 TYR     1      15.410  20.380  20.810  0.00  0.00
+ATOM     13  HD2 TYR     1      16.400  20.400  20.930  0.00  0.00
+ATOM     14  CE1 TYR     1      12.750  20.450  20.460  0.00  0.00
+ATOM     15  HE1 TYR     1      11.770  20.280  20.380  0.00  0.00
+ATOM     16  CE2 TYR     1      14.720  21.530  20.470  0.00  0.00
+ATOM     17  HE2 TYR     1      15.440  22.220  20.420  0.00  0.00
+ATOM     18  CZ  TYR     1      13.520  21.590  20.310  0.00  0.00
+ATOM     19  OH  TYR     1      13.060  22.530  20.050  0.00  0.00
+ATOM     20  HH  TYR     1      12.910  23.490  19.830  0.00  0.00
+ATOM     21  C   TYR     1      17.370  16.950  20.090  0.00  0.00
+ATOM     22  O   TYR     1      17.890  15.850  20.090  0.00  0.00
+ATOM     23  N   ALA     2      18.030  18.130  20.090  0.00  0.00
+ATOM     24  H   ALA     2      17.550  19.000  20.090  0.00  0.00
+ATOM     25  CA  ALA     2      19.490  18.080  20.090  0.00  0.00
+ATOM     26  HA  ALA     2      19.760  17.610  20.930  0.00  0.00
+ATOM     27  CB  ALA     2      19.940  17.310  18.850  0.00  0.00
+ATOM     28  HB1 ALA     2      20.940  17.260  18.820  0.00  0.00
+ATOM     29  HB2 ALA     2      19.560  16.380  18.870  0.00  0.00
+ATOM     30  HB3 ALA     2      19.610  17.780  18.030  0.00  0.00
+ATOM     31  C   ALA     2      20.110  19.480  20.090  0.00  0.00
+ATOM     32  O   ALA     2      19.420  20.490  20.090  0.00  0.00
+ATOM     33  N   SER     3      21.450  19.460  20.090  0.00  0.00
+ATOM     34  H   SER     3      21.770  18.510  20.090  0.00  0.00
+ATOM     35  CA  SER     3      22.140  20.730  20.090  0.00  0.00
+ATOM     36  HA  SER     3      21.860  21.210  19.260  0.00  0.00
+ATOM     37  CB  SER     3      21.740  21.520  21.330  0.00  0.00
+ATOM     38  HB1 SER     3      20.760  21.700  21.340  0.00  0.00
+ATOM     39  HB2 SER     3      22.000  21.030  22.170  0.00  0.00
+ATOM     40  OG  SER     3      22.400  22.760  21.360  0.00  0.00
+ATOM     41  HG  SER     3      22.700  23.670  21.650  0.00  0.00
+ATOM     42  C   SER     3      23.650  20.490  20.090  0.00  0.00
+ATOM     43  O   SER     3      24.130  19.370  20.090  0.00  0.00
+ATOM     44  N   THR     4      24.370  21.630  20.090  0.00  0.00
+ATOM     45  H   THR     4      23.740  22.420  20.090  0.00  0.00
+ATOM     46  CA  THR     4      25.810  21.520  20.090  0.00  0.00
+ATOM     47  HA  THR     4      26.060  21.020  20.920  0.00  0.00
+ATOM     48  CB  THR     4      26.270  20.770  18.840  0.00  0.00
+ATOM     49  HB  THR     4      25.900  19.840  18.890  0.00  0.00
+ATOM     50  OG1 THR     4      27.670  20.650  18.820  0.00  0.00
+ATOM     51  HG1 THR     4      28.590  20.410  18.530  0.00  0.00
+ATOM     52  CG2 THR     4      25.850  21.460  17.540  0.00  0.00
+ATOM     53  HG21THR     4      26.170  20.930  16.760  0.00  0.00
+ATOM     54  HG22THR     4      24.850  21.540  17.510  0.00  0.00
+ATOM     55  HG23THR     4      26.250  22.380  17.510  0.00  0.00
+ATOM     56  C   THR     4      26.430  22.920  20.090  0.00  0.00
+ATOM     57  OT  THR     4      27.090  23.680  20.090  0.00  0.00
+ATOM     58  O   THR     4      25.740  23.940  20.090  0.00  0.00
+ATOM     59  HO  THR     4      25.430  24.890  20.090  0.00  0.00

GROMACS/nmr2/conf.gro

+"These Gromacs Guys Really Rock" (P.J. Meulenhoff)
+   59
+    1TYR      N    1   1.515   1.585   2.009
+    1TYR     H1    2   1.416   1.597   2.009
+    1TYR     H2    3   1.543   1.534   1.927
+    1TYR     CA    4   1.579   1.715   2.009
+    1TYR     HA    5   1.549   1.762   1.926
+    1TYR     CB    6   1.535   1.793   2.133
+    1TYR    HB1    7   1.472   1.737   2.186
+    1TYR    HB2    8   1.615   1.815   2.188
+    1TYR     CG    9   1.466   1.921   2.098
+    1TYR    CD1   10   1.329   1.927   2.079
+    1TYR    HD1   11   1.273   1.844   2.089
+    1TYR    CD2   12   1.535   2.040   2.081
+    1TYR    HD2   13   1.634   2.043   2.093
+    1TYR    CE1   14   1.269   2.047   2.046
+    1TYR    HE1   15   1.171   2.030   2.038
+    1TYR    CE2   16   1.466   2.155   2.047
+    1TYR    HE2   17   1.538   2.224   2.040
+    1TYR     CZ   18   1.346   2.161   2.031
+    1TYR     OH   19   1.300   2.255   2.005
+    1TYR     HH   20   1.285   2.351   1.982
+    1TYR      C   21   1.731   1.697   2.009
+    1TYR      O   22   1.783   1.587   2.009
+    2ALA      N   23   1.797   1.815   2.009
+    2ALA      H   24   1.748   1.902   2.009
+    2ALA     CA   25   1.943   1.810   2.009
+    2ALA     HA   26   1.970   1.764   2.094
+    2ALA     CB   27   1.988   1.733   1.885
+    2ALA    HB1   28   2.088   1.728   1.883
+    2ALA    HB2   29   1.950   1.640   1.888
+    2ALA    HB3   30   1.955   1.780   1.803
+    2ALA      C   31   2.005   1.950   2.009
+    2ALA      O   32   1.936   2.051   2.009
+    3SER      N   33   2.139   1.948   2.009
+    3SER      H   34   2.171   1.853   2.009
+    3SER     CA   35   2.208   2.075   2.009
+    3SER     HA   36   2.180   2.123   1.926
+    3SER     CB   37   2.168   2.154   2.133
+    3SER    HB1   38   2.070   2.172   2.133
+    3SER    HB2   39   2.193   2.105   2.216
+    3SER     OG   40   2.234   2.278   2.136
+    3SER     HG   41   2.264   2.369   2.165
+    3SER      C   42   2.359   2.051   2.009
+    3SER      O   43   2.407   1.939   2.009
+    4THR      N   44   2.431   2.165   2.009
+    4THR      H   45   2.369   2.244   2.009
+    4THR     CA   46   2.575   2.154   2.009
+    4THR     HA   47   2.599   2.104   2.092
+    4THR     CB   48   2.621   2.079   1.884
+    4THR     HB   49   2.584   1.986   1.889
+    4THR    OG1   50   2.761   2.067   1.882
+    4THR    HG1   51   2.854   2.044   1.854
+    4THR    CG2   52   2.579   2.148   1.754
+    4THR   HG21   53   2.612   2.095   1.676
+    4THR   HG22   54   2.479   2.155   1.750
+    4THR   HG23   55   2.619   2.240   1.751
+    4THR      C   56   2.637   2.294   2.009
+    4THR     OT   57   2.702   2.370   2.009
+    4THR      O   58   2.703   2.370   2.009
+    4THR     HO   59   2.762   2.451   2.009
+   4.00000   4.00000   4.00000

GROMACS/nmr2/genconf.gcp

+;
+;	User spoel (20016)
+;	Thu Sep 12 14:12:41 1996
+;	Input file
+;
+nx                  =  2
+ny                  =  1
+nz                  =  1
+dx                  =  0.0000
+dy                  =  0.0000
+dz                  =  0.0000
+seed                =  1993
+max_x_rotation      =  0.000000
+max_y_rotation      =  0.000000
+max_z_rotation      =  0.000000
+max_x_translation   =  0.000000
+max_y_translation   =  0.000000
+max_z_translation   =  0.000000

GROMACS/nmr2/grompp.mdp

+;
+;	File 'mdout.mdp' was generated
+;	By user: erik (214)
+;	On host: gaugain.theophys.kth.se
+;	At date: Tue May 15 20:00:22 2001
+;
+
+; VARIOUS PREPROCESSING OPTIONS = 
+title                    = Yo
+cpp                      = /usr/bin/cpp
+include                  = -I../top
+define                   = 
+
+; RUN CONTROL PARAMETERS = 
+integrator               = md
+; start time and timestep in ps = 
+tinit                    = 0.0
+dt                       = 0.002
+nsteps                   = 5000
+; number of steps for center of mass motion removal = 
+nstcomm                  = 1
+comm-grps                = 
+
+; LANGEVIN DYNAMICS OPTIONS = 
+; Temperature, friction coefficient (amu/ps) and random seed = 
+bd-temp                  = 300
+bd-fric                  = 0
+ld-seed                  = 1993
+
+; ENERGY MINIMIZATION OPTIONS = 
+; Force tolerance and initial step-size = 
+emtol                    = 0.001
+emstep                   = 0.1
+; Max number of iterations in relax_shells = 
+niter                    = 0
+; Frequency of steepest descents steps when doing CG = 
+nstcgsteep               = 1000
+
+; OUTPUT CONTROL OPTIONS = 
+; Output frequency for coords (x), velocities (v) and forces (f) = 
+nstxout                  = 10
+nstvout                  = 0
+nstfout                  = 0
+; Output frequency for energies to log file and energy file = 
+nstlog                   = 100
+nstenergy                = 100
+; Output frequency and precision for xtc file = 
+nstxtcout                = 10
+xtc_precision            = 1000
+; This selects the subset of atoms for the xtc file. You can = 
+; select multiple groups. By default all atoms will be written. = 
+xtc-grps                 = 
+; Selection of energy groups = 
+energygrps               = System
+
+; NEIGHBORSEARCHING PARAMETERS = 
+; nblist update frequency = 
+nstlist                  = 100
+; ns algorithm (simple or grid) = 
+ns_type                  = simple
+; Periodic boundary conditions: xyz or none = 
+pbc                      = xyz
+; nblist cut-off         = 
+rlist                    = 1
+domain-decomposition     = no
+
+; OPTIONS FOR ELECTROSTATICS AND VDW = 
+; Method for doing electrostatics = 
+coulombtype              = Cut-off
+rcoulomb-switch          = 0
+rcoulomb                 = 1
+; Dielectric constant (DC) for cut-off or DC of reaction field = 
+epsilon_r                = 1.0
+; Method for doing Van der Waals = 
+vdw-type                 = Cut-off
+; cut-off lengths        = 
+rvdw-switch              = 0
+rvdw                     = 1
+; Apply long range dispersion corrections for Energy and Pressure = 
+DispCorr                 = no
+; Spacing for the PME/PPPM FFT grid = 
+fourierspacing           = 0.12
+; FFT grid size, when a value is 0 fourierspacing will be used = 
+fourier_nx               = 0
+fourier_ny               = 0
+fourier_nz               = 0
+; EWALD/PME/PPPM parameters = 
+pme_order                = 4
+ewald_rtol               = 1e-05
+epsilon_surface          = 0
+optimize_fft             = no
+
+; OPTIONS FOR WEAK COUPLING ALGORITHMS = 
+; Temperature coupling   = 
+tcoupl                   = berendsen
+; Groups to couple separately = 
+tc-grps                  = System
+; Time constant (ps) and reference temperature (K) = 
+tau_t                    = 0.1
+ref_t                    = 300
+; Pressure coupling      = 
+Pcoupl                   = no
+Pcoupltype               = Isotropic
+; Time constant (ps), compressibility (1/bar) and reference P (bar) = 
+tau_p                    = 1
+compressibility          = 
+ref_p                    = 1.0	1.0	1.0
+
+; SIMULATED ANNEALING CONTROL = 
+annealing                = no
+; Time at which temperature should be zero (ps) = 
+zero-temp_time           = 0
+
+; GENERATE VELOCITIES FOR STARTUP RUN = 
+gen_vel                  = yes
+gen_temp                 = 300.0
+gen_seed                 = 173529
+
+; OPTIONS FOR BONDS     = 
+constraints              = none
+; Type of constraint algorithm = 
+constraint-algorithm     = Lincs
+; Do not constrain the start configuration = 
+unconstrained-start      = no
+; Relative tolerance of shake = 
+shake-tol                = 1e-04
+; Highest order in the expansion of the constraint coupling matrix = 
+lincs-order              = 4
+; Lincs will write a warning to the stderr if in one step a bond = 
+; rotates over more degrees than = 
+lincs-warnangle          = 30
+; Convert harmonic bonds to morse potentials = 
+morse                    = no
+
+; NMR refinement stuff  = 
+; Distance restraints type: No, Simple or Ensemble = 
+disre                    = Simple
+; Force weighting of pairs in one distance restraint: Equal or Conservative = 
+disre-weighting          = Equal
+; Use sqrt of the time averaged times the instantaneous violation = 
+disre-mixed              = no
+disre_fc                 = 1000
+disre_tau                = 0.0
+; Output frequency for pair distances to energy file = 
+nstdisreout              = 100
+
+; Free energy control stuff = 
+free-energy              = no
+init-lambda              = 0
+delta-lambda             = 0
+sc-alpha                 = 0
+sc-sigma                 = 0.3
+
+; Non-equilibrium MD stuff = 
+acc-grps                 = 
+accelerate               = 
+freezegrps               = 
+freezedim                = 
+cos-acceleration         = 0
+energygrp_excl           = 
+
+; Electric fields       = 
+; Format is number of terms (int) and for all terms an amplitude (real) = 
+; and a phase angle (real) = 
+E-x                      = 
+E-xt                     = 
+E-y                      = 
+E-yt                     = 
+E-z                      = 
+E-zt                     = 
+
+; User defined thingies = 
+user1-grps               = 
+user2-grps               = 
+userint1                 = 0
+userint2                 = 0
+userint3                 = 0
+userint4                 = 0
+userreal1                = 0
+userreal2                = 0
+userreal3                = 0
+userreal4                = 0

GROMACS/nmr2/pep.pdb

+ATOM      1  N   TYR     1      15.210  15.830  20.090  0.00  0.00
+ATOM      2  H1  TYR     1      14.210  15.950  20.090  0.00  0.00
+ATOM      3  H2  TYR     1      15.480  15.330  19.270  0.00  0.00
+ATOM      4  CA  TYR     1      15.850  17.130  20.090  0.00  0.00
+ATOM      5  HA  TYR     1      15.550  17.600  19.260  0.00  0.00
+ATOM      6  CB  TYR     1      15.410  17.910  21.330  0.00  0.00
+ATOM      7  HB1 TYR     1      14.790  17.350  21.870  0.00  0.00
+ATOM      8  HB2 TYR     1      16.220  18.130  21.880  0.00  0.00
+ATOM      9  CG  TYR     1      14.720  19.190  20.980  0.00  0.00
+ATOM     10  CD1 TYR     1      13.350  19.250  20.790  0.00  0.00
+ATOM     11  HD1 TYR     1      12.790  18.430  20.900  0.00  0.00
+ATOM     12  CD2 TYR     1      15.410  20.380  20.810  0.00  0.00
+ATOM     13  HD2 TYR     1      16.400  20.400  20.930  0.00  0.00
+ATOM     14  CE1 TYR     1      12.750  20.450  20.460  0.00  0.00
+ATOM     15  HE1 TYR     1      11.770  20.280  20.380  0.00  0.00
+ATOM     16  CE2 TYR     1      14.720  21.530  20.470  0.00  0.00
+ATOM     17  HE2 TYR     1      15.440  22.220  20.420  0.00  0.00
+ATOM     18  CZ  TYR     1      13.520  21.590  20.310  0.00  0.00
+ATOM     19  OH  TYR     1      13.060  22.530  20.050  0.00  0.00
+ATOM     20  HH  TYR     1      12.910  23.490  19.830  0.00  0.00
+ATOM     21  C   TYR     1      17.370  16.950  20.090  0.00  0.00
+ATOM     22  O   TYR     1      17.890  15.850  20.090  0.00  0.00
+ATOM     23  N   ALA     2      18.030  18.130  20.090  0.00  0.00
+ATOM     24  H   ALA     2      17.550  19.000  20.090  0.00  0.00
+ATOM     25  CA  ALA     2      19.490  18.080  20.090  0.00  0.00
+ATOM     26  HA  ALA     2      19.760  17.610  20.930  0.00  0.00
+ATOM     27  CB  ALA     2      19.940  17.310  18.850  0.00  0.00
+ATOM     28  HB1 ALA     2      20.940  17.260  18.820  0.00  0.00
+ATOM     29  HB2 ALA     2      19.560  16.380  18.870  0.00  0.00
+ATOM     30  HB3 ALA     2      19.610  17.780  18.030  0.00  0.00
+ATOM     31  C   ALA     2      20.110  19.480  20.090  0.00  0.00
+ATOM     32  O   ALA     2      19.420  20.490  20.090  0.00  0.00
+ATOM     33  N   SER     3      21.450  19.460  20.090  0.00  0.00
+ATOM     34  H   SER     3      21.770  18.510  20.090  0.00  0.00
+ATOM     35  CA  SER     3      22.140  20.730  20.090  0.00  0.00
+ATOM     36  HA  SER     3      21.860  21.210  19.260  0.00  0.00
+ATOM     37  CB  SER     3      21.740  21.520  21.330  0.00  0.00
+ATOM     38  HB1 SER     3      20.760  21.700  21.340  0.00  0.00
+ATOM     39  HB2 SER     3      22.000  21.030  22.170  0.00  0.00
+ATOM     40  OG  SER     3      22.400  22.760  21.360  0.00  0.00
+ATOM     41  HG  SER     3      22.700  23.670  21.650  0.00  0.00
+ATOM     42  C   SER     3      23.650  20.490  20.090  0.00  0.00
+ATOM     43  O   SER     3      24.130  19.370  20.090  0.00  0.00
+ATOM     44  N   THR     4      24.370  21.630  20.090  0.00  0.00
+ATOM     45  H   THR     4      23.740  22.420  20.090  0.00  0.00
+ATOM     46  CA  THR     4      25.810  21.520  20.090  0.00  0.00
+ATOM     47  HA  THR     4      26.060  21.020  20.920  0.00  0.00
+ATOM     48  CB  THR     4      26.270  20.770  18.840  0.00  0.00
+ATOM     49  HB  THR     4      25.900  19.840  18.890  0.00  0.00
+ATOM     50  OG1 THR     4      27.670  20.650  18.820  0.00  0.00
+ATOM     51  HG1 THR     4      28.590  20.410  18.530  0.00  0.00
+ATOM     52  CG2 THR     4      25.850  21.460  17.540  0.00  0.00
+ATOM     53  HG21THR     4      26.170  20.930  16.760  0.00  0.00
+ATOM     54  HG22THR     4      24.850  21.540  17.510  0.00  0.00
+ATOM     55  HG23THR     4      26.250  22.380  17.510  0.00  0.00
+ATOM     56  C   THR     4      26.430  22.920  20.090  0.00  0.00
+ATOM     57  O   THR     4      27.090  23.680  20.090  0.00  0.00

GROMACS/speptide/em.mdp

+;
+;	User spoel (236)
+;	Wed Nov  3 17:12:44 1993
+;	Input file
+;
+cpp                 =  /usr/bin/cpp
+define              =  -DFLEX_SPC
+constraints         =  none
+integrator          =  steep
+nsteps              =  100
+;
+;	Energy minimizing stuff
+;
+emtol               =  2000
+emstep              =  0.01
+
+nstcomm             =  1
+ns_type             =  grid
+rlist               =  1
+rcoulomb            =  1.0
+rvdw                =  1.0
+Tcoupl              =  no
+Pcoupl              =  no
+gen_vel             =  no

GROMACS/speptide/full.mdp

+;
+;	User spoel (236)
+;	Wed Nov  3 17:12:44 1993
+;	Input file
+;
+title               =  Yo
+cpp                 =  /usr/bin/cpp
+constraints         =  all-bonds
+integrator          =  md
+dt                  =  0.002	; ps !
+nsteps              =  5000	; total 10 ps.
+nstcomm             =  1
+nstxout             =  250
+nstvout             =  1000
+nstfout             =  0
+nstlog              =  100
+nstenergy           =  100
+nstlist             =  10
+ns_type             =  grid
+rlist               =  1.0
+rcoulomb            =  1.0
+rvdw                =  1.0
+; Berendsen temperature coupling is on in two groups
+Tcoupl              =  berendsen
+tc-grps		    =  Protein	SOL
+tau_t               =  0.1	0.1
+ref_t               =  300	300
+; Energy monitoring
+energygrps          =  Protein  SOL
+; Isotropic pressure coupling is now on
+Pcoupl              =  berendsen
+Pcoupltype          = isotropic
+tau_p               =  0.5
+compressibility     =  4.5e-5
+ref_p               =  1.0
+; Generate velocites is off at 300 K.
+gen_vel             =  no
+gen_temp            =  300.0
+gen_seed            =  173529
+

GROMACS/speptide/pr.mdp

+;
+;	User spoel (236)
+;	Wed Nov  3 17:12:44 1993
+;	Input file
+;
+title               =  Yo
+cpp                 =  /usr/bin/cpp
+define              =  -DPOSRES
+constraints         =  all-bonds
+integrator          =  md
+dt                  =  0.002	; ps !
+nsteps              =  5000	; total 10 ps.
+nstcomm             =  1
+nstxout             =  50
+nstvout             =  1000
+nstfout             =  0
+nstlog              =  10
+nstenergy           =  10
+nstlist             =  10
+ns_type             =  grid
+rlist               =  1.0
+rcoulomb            =  1.0
+rvdw                =  1.0
+; Berendsen temperature coupling is on in two groups
+Tcoupl              =  berendsen
+tc-grps		    =  Protein	SOL
+tau_t               =  0.1	0.1
+ref_t               =  300	300
+; Energy monitoring
+energygrps	    =  Protein	SOL
+; Pressure coupling is not on
+Pcoupl              =  no
+tau_p               =  0.5
+compressibility     =  4.5e-5
+ref_p               =  1.0
+; Generate velocites is on at 300 K.
+gen_vel             =  yes
+gen_temp            =  300.0
+gen_seed            =  173529