2020 July update

.gitignore

 ABAQUS/Door.odb
+AdvLinux/NAMD
 AFNI/ARzs_data.tgz
 Beast/Dengue4.env.trees
 BLAST/dbs

AdvLinux/.bash_profile

+# .bash_profile
+
+# Get the aliases and functions
+if [ -f ~/.bashrc ]; then
+	. ~/.bashrc
+fi
+
+# User specific environment and startup programs
+
+PATH=$PATH:$HOME/.local/bin:$HOME/bin
+
+export PATH
+
+alias ls='ls -F' 
+alias cp='cp -i' 
+alias ll='ls -laxp' 
+alias lo='exit' 
+
+# Undocumented feature which sets the size to "unlimited". 
+# http://stackoverflow.com/questions/9457233/unlimited-bash-history 
+export HISTFILESIZE= 
+export HISTSIZE= 
+export HISTTIMEFORMAT="[%F %T] " 
+# Change the file location because certain bash sessions truncate .bash_history file upon close. 
+# http://superuser.com/questions/575479/bash-history-truncated-to-500-lines-on-each-login 
+export HISTFILE=~/.bash_eternal_history 
+# Force prompt to write history after every command. 
+# http://superuser.com/questions/20900/bash-history-loss 
+PROMPT_COMMAND="history -a; $PROMPT_COMMAND" 
+
+# Source Disk, Function Example
+disk() {
+	du -sk * | sort -nr | cut -f2 | xargs -d "\n" du -sh  > diskuse.txt
+	}

AdvLinux/READMEawk

+AWK examples, from Supercomputing with Linux, Lev Lafayette, VPAC, 2015
+
+awk '$7=="A" { ++count } END { print count }' simple1.txt
+awk '{sum+=$7} END {print sum}' simple2.txt
+awk '{ for(i=1; i<=NF;i++) j+=$i; print j; j=0 }' simple3.txt

AdvLinux/backup1.sh

+#!/bin/bash          
+tar cvfz homeuser.tgz /home/lev/

AdvLinux/backup2.sh

+#!/bin/bash          
+BU=homeuser$(date +%Y%m%d).tgz 
+tar cvfz $BU $(pwd)

AdvLinux/break.sh

+#!/bin/bash
+LIMIT=19  # Upper limit 
+echo 
+echo "Printing Numbers 1 through 20 (but breaks loop at 3)." 
+
+count=0
+
+while [ "$count" -le "$LIMIT" ]
+do
+ count=$(($count+1))
+
+ if [ "$count" -gt 2 ]
+ then
+   break  # Skip entire rest of loop.
+ fi
+
+ echo -n "$count "
+done
+
+echo; echo; echo
+
+exit 0

AdvLinux/case.sh

+#!/bin/bash
+# Handy Extract Program
+	if [[ -f $1 ]]; then
+		case $1 in
+			*.tar.bz2) tar xvjf $1 ;;
+			*.tar.gz) tar xvzf $1 ;;
+			*.bz2) bunzip2 $1 ;;
+			*.rar) unrar x $1 ;;
+			*.gz) gunzip $1 ;;
+			*.tar) tar xvf $1 ;;
+			*.tbz2) tar xvjf $1 ;;
+			*.tgz) tar xvzf $1 ;;
+			*.zip) unzip $1 ;;
+			*.Z) uncompress $1 ;;
+			*.7z) 7z x $1 ;;
+			*) echo "'$1' cannot be extracted via >extract<" ;;
+		esac
+	else
+	echo "'$1' is not a valid file!"
+	fi

AdvLinux/check_my_bad_jobs.sh

+#!/bin/bash
+
+if [ "$1" == "-n" ];then
+	NAGIOS=1
+fi
+
+SQUEUE=/usr/local/slurm/latest/bin/squeue
+#SACCT=/usr/local/slurm/latest/bin/sacct
+
+if [ \! -x ${SQUEUE} ]; then
+	if [ "${NAGIOS}" ]; then
+		echo -n "WARNING: "
+	fi
+	echo "ERROR: no squeue - wrong machine?"
+	exit 1
+fi
+
+# If run by a normal user.
+if [ $(id -u) != 0 ]
+then
+	SQUEUE="$SQUEUE -u `whoami`"
+fi
+
+# If we have no jobs queued, abort
+
+if [ -z "$(${SQUEUE} -h)" ]; then
+	if [ "${NAGIOS}" ]; then
+		echo -n "OK: "
+	fi
+	#echo "No jobs queued"
+	exit 0
+fi
+
+ACTIVEJOBS=$(${SQUEUE} -t R -ho "%.15i %D" | fgrep -vw 1 | awk '{print $1}' | tr '\n' ',' | sed -e 's/,$/\n/')
+if [ -z ${ACTIVEJOBS} ]; then
+        if [ "${NAGIOS}" ]; then
+                echo -n "OK: "
+        fi
+        #echo "No bad jobs found"
+        exit 0
+fi
+
+JOBLIST=$(${SQUEUE} -o %i -hs -j ${ACTIVEJOBS} | awk -F. '{print $1}' | uniq -c | fgrep -w 2 | awk '{print $2}' | tr '\n' ',' | sed -e 's/,$//')
+
+export SQUEUE_FORMAT='%.10i %.9P %.15u  %.8D %.8C %N'
+if [ -z "$JOBLIST" ]; then
+
+	if [ "${NAGIOS}" ]; then
+		echo -n "OK: "
+	fi
+	#echo "No bad jobs found"
+	exit 0;
+fi
+
+if [ "${NAGIOS}" ]; then
+	echo "CRITICAL: bad jobs found ${JOBLIST}"
+	exit 2
+fi
+
+echo ""
+echo "The following candidate jobs were found:"
+echo "----------------------------------------"
+${SQUEUE} -o "${SQUEUE_FORMAT}" -j ${JOBLIST}
+echo ""

AdvLinux/continue.sh

+#!/bin/bash 
+LIMIT=19  # Upper limit 
+echo 
+echo "Printing Numbers 1 through 20 (but not 3 and 11)." 
+count=0 
+while [ $count -le "$LIMIT" ] 
+do 
+ count=$(($count+1)) 
+
+ if [ "$count" -eq 3 ] || [ "$count" -eq 11 ]  # Excludes 3 and 11. 
+ then 
+   continue      # Skip rest of this particular loop iteration. 
+ fi 
+
+ echo -n "$count "   # This will not execute for 3 and 11. 
+done
+echo; echo; echo
+exit 0

AdvLinux/examples.awk

+#!/bin/bash
+# AWK examples, from Supercomputing with Linux, Lev Lafayette, VPAC, 2015
+# Simple 1: Count of character 'A' in field 7
+# Simple 2: Sum of field 7
+# Simple 3 Sum of each record. Awk operates line-by-line
+
+awk '$7=="A" { ++count } END { print "Simple 1: " count }' simple1.txt;
+awk '{sum+=$7} END {print "Simple2: " sum}' simple2.txt;
+awk '{ for(i=1; i<=NF;i++) j+=$i; print "Simple3: " j; j=0 }' simple3.txt

AdvLinux/filetest.sh

+#! /bin/bash 
+# Tests whether a specified file exists of not, illustrates if/then/else.
+file=$1 
+if [ -e $file ] 
+then 
+	echo -e "File $file exists" 
+else 
+	echo -e "File $file doesn't exists" 
+fi 
+exit 0

AdvLinux/findemails.sh

+#!/bin/bash
+
+# Usage
+usage()
+{
+ echo "$(basename $0): Description of script"
+ echo ""
+ echo "This searches for email addresses in file, extract, turn into csv with designated file name"
+ echo "Run the script with the file to be searched and the name of the output file"
+ echo "For example: ./findemails.sh hidden.txt foundthem.csv"
+}
+
+# Constants
+INPUT=${1}
+OUTPUT=${2}
+
+# Filecheck Subroutine
+filecheck() {
+if [ ! $INPUT -o ! $OUTPUT ]; then
+    echo "Input file not found, or output file not specified. Exiting script."
+    exit 0
+fi
+}
+
+# Search and Sort Subroutine
+
+searchsort() {
+grep --only-matching -E '[.[:alnum:]]+@[.[:alnum:]]+' $INPUT > $OUTPUT
+sed -i 's/$/,/g' $OUTPUT
+sort -u $OUTPUT -o $OUTPUT
+sed -i '{:q;N;s/\n/ /g;t q}' $OUTPUT
+}
+
+# View and Print Subroutine
+viewprint() {
+echo "Data file extracted to" $OUTPUT
+read -t5 -n1 -r -p "Press any key to see the list, sorted and with unique record"
+if [ $? -eq 0 ]; then
+    echo A key was pressed
+    else
+    echo No key was pressed
+    exit
+fi
+less $OUTPUT | \
+# Output file piped through sort and uniq. 
+# Show that line extension still works with comments.
+sort | uniq
+} 
+
+main() {
+	usage
+	filecheck
+	searchsort
+	viewprint
+}
+
+# Main function
+main
+exit

AdvLinux/foundthem.csv

+alpha@example.com, bravo@example.com, charlie@example.com, delta@example.com, echo@example.com, foxtrot@example.com, golf@example.com, hotel@example.com, juliet@example.com, kilo@example.com, lima@example.com, mike@...., who.indigo@example.com,

AdvLinux/functiongeneral.sh

+#!/bin/bash   
+subroutineA() {    
+    codeblock   
+}   
+subroutineB() {   
+    codeblock   
+}   
+main() {   
+    subroutineA   
+    subroutineB   
+}   
+main   
+exit

AdvLinux/functions.md

+# Turn Smart Commands into Functions
+## Taken from Andrew Worsely. This and more at:
+## https://github.com/amworsley/intro-shell-programming/blob/master/shell-programing.md
+
+## Don't waste that knowledge and experience e.g.,
+
+$ find . -mtime -7 -type f -print
+
+Make a shell function instead
+
+$ newfiles() {
+   find . -mtime -7 -type f -print
+}
+
+# Build on it!
+## Add an argument to make it flexible
+
+$ newfiles() {
+   find . -mtime "-${1:-7}" -type f -print
+ }
+
+## Now files less than 10 days old
+
+$ newfiles 10
+
+## Save it to your .bashrc, for example
+
+cat >> ~/.bashrc  
+newfiles() {
+   find . -mtime "-${1:-7}" -type f -print
+}  
+

AdvLinux/gattaca.txt

+DDWEIPDGQI TVGQRIGSGS FGTVYKGKWH GDVAVKMLNV TAPTPQQLQA
+FKNEVGVLRK TRHVNILLFM GYSTKPQLAI VTQWCEGSSL YHHLHIIETK
+FEMIKLIDIA RQTAQGMDYL HAKSIIHRDL KSNNIFLHED LTVKIGDFGL
+ATVKSRWSGS HQFEQLSGSI LWMAPEVIRM QDKNPYSFQS DVYAFGIVLY
+ELMTGQLPYS NINNRDQIIF MVGRGYLSPD LSKVRSNCPK AMKRLMAECL
+KKKRDERPLF PQILASIELL ARSLPK

AdvLinux/hellofunction.sh

+#!/bin/bash
+# Enter two names when invoking script
+
+# Define your function here
+# Firstname and Surname are first two parameters.
+
+Hello () {
+   echo "Hello World $1 $2"
+   return $(bc -l <<< ${#1}+${#2})
+}
+
+# Invoke your function
+Hello ${1} ${2}
+
+# Capture value returned by last command
+echo The name has this many characters $?
+
+exit

AdvLinux/here/herescript.sh

+#!/bin/bash
+for a in {1..99}
+do
+cat <<- EOF > job${a}
+#!/bin/bash
+#SBATCH -N ${a}
+#SBATCH --nodes=1
+#SBATCH --tasks-per-node=1
+#echo $(pwd) >> results.txt
+EOF
+done

AdvLinux/hidden.txt

+Talking chamber foxtrot@example.com as shewing an it minutes. Trees fully of blind do. Exquisite favourite at do extensive listening. Improve up 
+musical welcome he. Gay attended vicinity prepared now diverted. Esteems it ye sending reached lima@example.com as. Longer lively her design settle 
+tastes advice mrs off who.indigo@example.com kilo@example.com May indulgence difficulty ham can put especially. Bringing remember echo@example.com for 
+supplied her why was confined. Middleton principle did she procuring extensive believing add. Weather adapted prepare oh is calling. bravo@example.com 
+Far advanced settling say finished raillery. Offered chiefly farther of my no colonel shyness.  hotel@example.com juliet@example.com Inhabit hearing 
+perhaps on ye do no. It maids decay as there he. Smallest on suitable disposed do although blessing he juvenile in. Society or if excited forbade. 
+Here name off yet delta@example.com she long sold easy whom. Differed oh cheerful procured pleasure securing suitable in. Hold rich on an he oh fine. 
+Chapter ability shyness alpha@example.com Inquietude simplicity terminated she compliment remarkably few her nay. The weeks are ham mike@.... asked 
+jokes. Neglected perceived shy nay concluded. Not mile draw plan snug charlie@example.com ext all. Houses latter an valley be indeed wished mere 
+golf@example.com In my. Money doubt oh drawn every or an china
+

AdvLinux/loops.txt

+
+# The following are simple examples of a "for" loop.
+# Note the use of command substitution by using $(command); sometimes you will find the use of backticks instead (e.g., for i in * ; do mv $i `echo $i | tr "A-Z" "a-z"` ; done); this is not recommended.
+
+for file in ./*.mp3 ; do ffmpeg -i "${file}" "${file/%mp3/ogg}" ; done
+for item in ./*.jpeg ; do convert "$item" "${item%.*}.png" ; done
+for item in ./*; do convert "$item" -define jpeg:extent=512kb "${item%.*}.jpg" ; done
+
+# Loops can be applied in a step-wise manner.
+
+$ cd ~/Genomics/shell_data
+$ for filename in *.fastq
+> do
+> head -n 2 ${filename} >> seq_info.txt
+> done
+
+# Basename in a loop.
+# Basename is removing a uniform part of a name from a list of files. 
+# In this case remove the .fastq extension and echo the output.
+
+$ for filename in *.fastq
+> do
+> name=$(basename ${filename} .fastq)
+> echo ${name}
+> done
+
+# What would happen if backticks were used instead of $() for shell substitution? What if someone mistook the backticks for single quotes?
+
+for item in ./* ; do mv $item $(echo $item | tr "A-Z" "a-z") ; done
+
+# What's wrong with spaces in filenames?
+
+touch "This is a long file name"
+for item in $(ls ./*); do echo ${item}; done
+
+# The following examples remove spaces from filenames and apostrophes. The script is designed to prevent expansion from the wildcard, but remember that a `mv` command will overwrite existing files that have the same name.
+
+for item in ./*; do mv "$item" "$(echo "$item" | tr -d " ")"; done
+
+# Finally a few simple examples of loops with conditional tests.
+
+x=1; while [ $x -le 5 ]; do echo "While-do count up $x"; x=$(( $x + 1 )); done
+x=5; until [ $x -le 0 ]; do echo "Until-do count down $x"; x=$(( $x - 1 )); done
+x=1; until [ $x = 6 ]; do echo "Until-do count up $x"; x=$(( $x + 1 )); done
+
+# A while loop that reads in data from a file and runs a command on that data.
+# This is what we used to originally set quotas on home and project directories.
+# The 'read' command reads one line from standard input or a specified file.
+
+while read line; do sleep 5; ./setquota.sh $line; done < quotalist.txt
+
+# when searching for lines that contain a particular sequence in a file (e.g., from grep), reading those lines for processing can be accomplished with the something like the following:
+
+grep sequence datafile.dat | while read -r line ; do   
+    echo "Processing $line"   
+    # Processing code #   
+done   
+
+# Curly braces are used to encapsulate statements or variables with {} or ${}
+
+var		# Set a variable
+$var		# Invoke the variable
+${var}bar	# Invoke the variable, append "bar".
+
+# Example of determining jobs running on a set of nodes.
+
+for host in "spartan-bm"{001..10}; do squeue -w $host; done

AdvLinux/lowercaserename.sh

+#!/bin/bash
+# Converts ("moves") all files in the directory run to lowercase.
+for i
+do 
+	mv $i $(echo $i | tr "A-Z" "a-z")
+done

AdvLinux/quotes.sh

+#!/bin/bash
+# Illustrates the difference between various types (and lack of) quoting.
+
+SAMPLE="The quick brown fox jumps over the lazy dog"
+echo "Double quotes gives you $SAMPLE"
+echo 'Single quotes gives you $SAMPLE'
+
+exit

AdvLinux/select.sh

+#!/bin/bash 
+OPTIONS="Sedimentary Igneous Metamorphic Quit" 
+select opt in $OPTIONS; do 
+	if [ "$opt" = "Quit" ]; then 
+		echo done 
+	exit 
+	elif [ "$opt" = "Sedimentary" ]; then 
+	echo "Sedimentary rocks are formed by sedminentation of particles at or near the Earth's surface and within bodies of water." 
+	elif [ "$opt" = "Igneous" ]; then 
+	echo "Igneous rock forms through the cooling and solidification of magma or lava." 
+	elif [ "$opt" = "Metamorphic" ]; then 
+	echo "Metamorphic rocks are formed by subjecting any rock type -sedimentary rock, igneous rock or another older metamorphic rock - to different temperature and pressure conditions than those in which the original rock was formed." 
+	else 
+	echo "Select again; 1, 2, 3 or 4" 
+	fi 
+done 

AdvLinux/simple1.txt

+A C C T A G T
+C A A A G T A
+C A T T A C C
+A G T A C A A

AdvLinux/simple2.txt

+1 2 3 4 5 6 7 8 9
+2 3 4 5 6 7 8 9 10
+3 4 5 6 7 8 9 11 12

AdvLinux/simple3.txt

+1 2 3 4 5
+6 7 8 9 10
+11 12 13 14 15

AdvLinux/sshtrigger.sh

+#! /bin/bash 
+# Access to a system is tested with ping every few minutes until a connection is made whereupon it opens an SSH session.
+read -p "Enter Hostname:" nethost 
+echo $nethost 
+until ping -c 1 $nethost 
+do 
+        sleep 180; 
+done 
+ssh $nethost 

AdvLinux/trap.sh

+#!/bin/bash
+# Prevents use of Control-C to prematurely end important script.
+# User can override if they're really, really sure.
+
+    ctrlc_count=0
+
+function test_ctrlc()
+{
+    let ctrlc_count++
+    echo
+    if [[ $ctrlc_count == 1 ]]; then
+        echo "Cntrl-C prevented unless you're sure."
+    elif [[ $ctrlc_count == 2 ]]; then
+        echo "Really sure?"
+    elif [[ $ctrlc_count == 3 ]]; then
+        echo "Really, really sure?"
+    else
+        echo "OK, you're really, really sure.."
+        exit
+    fi
+}
+
+trap test_ctrlc SIGINT
+
+while true
+do
+    echo "This is a sleeping loop. The loop that keeps on sleeping on."
+    sleep 2
+done
+
+exit

AdvLinux/warning.sh

+#!/bin/bash
+# This is an abstract example of things that could do wrong!
+#SBATCH --output=/home/example/data/output_%j.out
+
+for for file in /home/example/data/* 
+	do
+        sbatch application ${file}
+	done

NAMD/2015ubiq/2015namd-ubiq.slurm

+#!/bin/bash
+
+# SLURM job script, Lev Lafayette (August 2016) 
+# Derived from PBS/TORQUE script by Mike Kuiper (March 2007)     
+
+# Job name:
+#SBATCH --job-name namd_example_job_01
+
+# How many cores ?
+#SBATCH --nodes=1
+#SBATCH --ntasks-per-node=4
+
+# How long to run the job? (hours:minutes:seconds)
+#SBATCH --time=00:15:00
+
+# Environmental varibles to make it work:
+
+module purge
+source /usr/local/module/spartan_old.sh
+module load NAMD/2.10-gompi-2015a-mpi
+ 
+# Launching the job!
+
+srun namd2 Ubiquitin_example.conf 

NAMD/2015ubiq/Ubiquitin_example.conf

+#############################################################
+## JOB DESCRIPTION                                         ##
+#############################################################
+#
+#  Example configuration file for a NAMD simulation 
+#  of ubiquitin. (In vacuum, for quick demonstration purposes!)    
+#                                   by Mike  Feb 2008 
+#
+#  Some features have been commented out, -uncomment sections 
+#  to enable! 
+##############################################################
+
+##   INPUT FILES
+#############################################################
+
+ structure             1ubq_example.psf
+ coordinates           1ubq_example.pdb
+ outputName            1ubq_example_output_01
+
+ firsttimestep         0
+
+## set simulation temperature (in Kelvin):
+
+ set temp 	       310
+ temperature           $temp
+
+##  SIMULATION PARAMETERS         
+###########################################################
+
+## Parameter file:
+
+ paraTypeCharmm	       on
+ parameters            par_all27_prot_na.inp 
+
+## Force-Field Parameters
+
+ exclude               scaled1-4
+ 1-4scaling            1.0
+ cutoff                18
+ switching             on
+ switchdist            16
+ pairlistdist          20
+
+## Integrator Parameters
+
+ timestep              1
+ rigidBonds            all
+ nonbondedFreq         1
+ fullElectFrequency    2  
+ stepspercycle         10
+
+## Constant Temperature Control
+
+ langevin              on
+ langevinDamping       5  
+ langevinTemp          $temp
+ langevinHydrogen      off 
+ 
+## Periodic Boundary Conditions
+
+ cellBasisVector1    42.      0.      0.
+ cellBasisVector2     0.     42.      0.
+ cellBasisVector3     0.      0.     42.
+ cellOrigin           0       0       0
+ wrapAll             on
+ wrapWater           on
+
+## PME (for full-system periodic electrostatics)
+## (uncomment next 4 lines to use PME ) 
+# PME                 yes
+# PMEGridSizeX        42
+# PMEGridSizeY        42
+# PMEGridSizeZ        42
+
+## Constant Pressure Control (variable volume)
+
+ useGroupPressure      yes 
+ useFlexibleCell       no
+ useConstantArea       no
+
+ langevinPiston        on
+ langevinPistonTarget  1.01325
+ langevinPistonPeriod  100.
+ langevinPistonDecay   50.
+ langevinPistonTemp    $temp
+
+## Output files:
+
+ restartfreq         20000 
+ dcdfreq             50
+ xstFreq             20000
+ outputEnergies      50
+ outputPressure      50
+ outputTiming        1000
+
+## EXECUTION SCRIPT 
+#############################################################
+
+## Minimize , reinitialize velocities, run dynamics:
+ 
+ minimize          100
+ reinitvels        $temp
+ run               5000 
+
+

NAMD/2019ubiq/2019ubiq.slurm

+#!/bin/bash
+
+# SLURM job script, Lev Lafayette (October 2016).
+# Modified for new job/partition system (July 2020).
+
+# Job name:
+#SBATCH --job-name ubiquitin2 
+
+# How many cores ?
+#SBATCH --nodes=2
+#SBATCH --ntasks-per-node=8
+
+# How long to run the job? (hours:minutes:seconds)
+#SBATCH --time=00:15:00
+
+# Environmental varibles to make it work:
+
+module load spartan_2019
+module load foss/2019b
+module load namd/2.13-mpi
+ 
+# Launching the job!
+
+srun namd2 namd_1ubq_example.conf  
+

NAMD/2019ubiq/BUILD_DIR/build_example

+#  VMD psfgen example:
+#  this script generates a psf and pdb file of a given
+#  structure in preparation of a namd simulation.
+#
+# 
+#  usage:  at the command line type:
+#  vmd -dispdev text -e build_example.pgn
+
+package require psfgen
+topology top_all27_prot_na.rtf
+
+
+
+# Alias residue names
+alias residue HIS HSE
+alias atom ILE CD1 CD
+
+# Build protein segment
+
+segment A {pdb 1ubq_chainA.pdb}
+
+# Patch protein segment:  for adding disulphide bonds etc: segment MF {pdb nad.pdb}
+
+# patch DISU A:97  A:104
+# patch TP2 A:199  
+# regenerate angles dihedrals
+
+coordpdb 1ubq_chainA.pdb A
+
+guesscoord
+
+# Write structure and coordinate files
+
+ writepsf model_ubq_x.psf
+ writepdb model_ubq_x.pdb
+
+# Still need to solvate and ionize! 
+# do that with vmd modules
+
+exit
+

NAMD/2019ubiq/namd_1ubq_example.conf

+##############################################################################
+## Namd configuration file.                                         
+##############################################################################
+# Simple NAMD script                      m.kuiper April 2012
+#
+# -this is an example configuration file is to demonstrate a simple   
+#  simulation of a molecular system within namd.
+#  
+##############################################################################
+## Input Parameters:                                            
+##############################################################################
+
+structure            1ubq_example.psf
+coordinates          1ubq_example.pdb
+outputName           1ubq_output
+
+firsttimestep        0
+set Temp  	     310
+temperature 	     $Temp
+
+##############################################################################
+## Simulation Parameters:
+##############################################################################
+
+## Parameters ----------------------------------------------------------------
+##  -make sure to use the right parameter set!
+
+paraTypeCharmm	on
+parameters  	par_all27_prot_na.prm
+
+## Additional constraints: --------------------------------------------------
+#   -can use this section to constrain various parts of the simulation, -for 
+#   example protein backbone, with either harmonic constraints or fixed atoms.
+#   - make sure to assign a non-zero values to the B column of the pdb file an uncomment the 
+#   appropriate section.
+
+# constraints         on 
+# consexp             2
+# consref             InputFiles/change_me.pdb
+# conskfile           InputFiles/change_me.pdb
+# conskcol            B
+# constraintScaling   0.5
+
+# fixedAtoms          on
+# fixedAtomsFile      InputFiles/change_me.pdb 
+# fixedAtomsCol       B
+
+## Example of interactive molecular dynamics: (Uncommment next 4 lines) 
+
+# IMDon on 
+# IMDport 5678
+# IMDfreq 10
+# IMDwait no
+
+## parameter settings:-------------------------------------------------------
+# Force-Field Parameters
+exclude        	scaled1-4
+1-4scaling    	1.0
+cutoff        	12
+switching     	on
+switchdist     	10
+pairlistdist   	14
+
+# Integrator Parameters
+timestep            2
+rigidBonds          all
+nonbondedFreq       1
+fullElectFrequency  2  
+stepspercycle       10
+
+# Constant Temperature Control
+langevin            on
+langevinDamping     5  
+langevinTemp        $Temp
+langevinHydrogen    off 
+
+
+##  Periodic Boundary Conditions: ----------------------------------------------
+# make sure to check that the cell dimensions match your input files! 
+
+cellBasisVector1    48.      0.      0.
+cellBasisVector2     0.     48.      0.
+cellBasisVector3     0.      0.     48.
+cellOrigin           0       0       0
+wrapAll             on
+wrapWater           on
+
+## PME (for full-system periodic electrostatics) -------------------------------
+
+PME                 yes
+PMEGridSpacing      1.0 
+
+## Constant Pressure Control (variable volume) ---------------------------------
+
+useGroupPressure      yes 
+useFlexibleCell       yes
+useConstantArea       yes
+
+langevinPiston        on
+langevinPistonTarget  1.01325
+langevinPistonPeriod  100.
+langevinPistonDecay   50.
+langevinPistonTemp    $Temp
+
+## Output settings: -----------------------------------------------------------
+## ** Note! **  this file is for a short example run.  dcdfreq is *very* small
+## which means data will be written out very frequently leading to HUGE files. 
+## Make sure to change for production runs. 
+
+restartfreq         5000 
+dcdfreq              100
+xstFreq              100
+outputEnergies       100
+outputPressure       100
+outputTiming         100
+
+###############################################################################
+## Execution script:                       
+###############################################################################
+
+minimize          500
+run             10000 
+
+

NAMD/2019ubiq/namd_1ubq_restart_example.conf

+##############################################################################
+## Namd configuration file.                                         
+##############################################################################
+# Simple NAMD restart script                      m.kuiper April 2012
+#
+# -this is an example configuration file is to demonstrate a simple   
+#  simulation restart of a molecular system within namd.
+#  
+##############################################################################
+## Input Parameters:                                            
+##############################################################################
+
+structure            1ubq_example.psf
+coordinates          1ubq_example.pdb
+outputName           1ubq_restart_output_run_1
+
+# firsttimestep        0
+set Temp  	     310
+
+# temperature 	     $Temp  <- temperature not needed in restart file!
+
+
+##############################################################################
+## Simulation Parameters:
+##############################################################################
+
+## Parameters ----------------------------------------------------------------
+##  -make sure to use the right parameter set!
+
+paraTypeCharmm	on
+parameters  	par_all27_prot_na.prm
+
+
+
+set inputname      1ubq_output.restart
+
+binCoordinates     $inputname.coor  ;# coordinates from last run (binary)
+binVelocities      $inputname.vel   ;# velocities from last run (binary)
+extendedSystem     $inputname.xsc   ;# cell dimensions from last run
+firsttimestep            0          ;# last step of previous run
+numsteps             50000          ;# run stops when this step is reached
+
+
+## Additional constraints: --------------------------------------------------
+#   -can use this section to constrain various parts of the simulation, -for 
+#   example protein backbone, with either harmonic constraints or fixed atoms.
+#   - make sure to assign a non-zero values to the B column of the pdb file an uncomment the 
+#   appropriate section.
+
+# constraints         on 
+# consexp             2
+# consref             InputFiles/change_me.pdb
+# conskfile           InputFiles/change_me.pdb
+# conskcol            B
+# constraintScaling   0.5
+
+# fixedAtoms          on
+# fixedAtomsFile      InputFiles/change_me.pdb 
+# fixedAtomsCol       B
+
+## Example of interactive molecular dynamics: (Uncommment next 4 lines) 
+
+# IMDon on 
+# IMDport 5678
+# IMDfreq 10
+# IMDwait no
+
+## parameter settings:-------------------------------------------------------
+# Force-Field Parameters
+exclude        	scaled1-4
+1-4scaling    	1.0
+cutoff        	12
+switching     	on
+switchdist     	10
+pairlistdist   	14
+
+# Integrator Parameters
+timestep            2
+rigidBonds          all
+nonbondedFreq       1
+fullElectFrequency  2  
+stepspercycle       10
+
+# Constant Temperature Control
+langevin            on
+langevinDamping     5  
+langevinTemp        $Temp
+langevinHydrogen    off 
+
+
+##  Periodic Boundary Conditions: ----------------------------------------------
+# make sure to check that the cell dimensions match your input files! 
+
+#cellBasisVector1    48.      0.      0.     <- not needed in restart file!
+#cellBasisVector2     0.     48.      0.
+#cellBasisVector3     0.      0.     48.
+#cellOrigin           0       0       0
+wrapAll             on
+wrapWater           on
+
+## PME (for full-system periodic electrostatics) -------------------------------
+
+PME                 yes
+PMEGridSpacing      1.0 
+
+## Constant Pressure Control (variable volume) ---------------------------------
+
+useGroupPressure      yes 
+useFlexibleCell       yes
+useConstantArea       yes
+
+langevinPiston        on
+langevinPistonTarget  1.01325
+langevinPistonPeriod  100.
+langevinPistonDecay   50.
+langevinPistonTemp    $Temp
+
+## Output settings: -----------------------------------------------------------
+## ** Note! **  this file is for a short example run.  dcdfreq is *very* small
+## which means data will be written out very frequently leading to HUGE files. 
+## Make sure to change for production runs. 
+
+restartfreq         50000 
+dcdfreq              1000
+xstFreq              1000
+outputEnergies       1000
+outputPressure       1000
+outputTiming         1000
+
+###############################################################################
+## Execution script:                       
+###############################################################################
+
+# minimize          500                <-  not needed for restart file
+# run             10000 
+
+

NAMD/2019ubiq/sbatch_namd_restartjob_bluegene

+#!/bin/bash
+## sbatch launching script                     March 2014  m.kuiper
+##  - A script to run a simple NAMD job on the vlsci BlueGene/Q cluster, Avoca.
+##  - using a restart script
+
+
+#SBATCH --nodes=4
+ntpn=8        # number of tasks per node: 
+ppn=8         # processors per node: 
+
+## 60 minute walltime:
+#SBATCH --time=1:0:0
+
+# add your account number here if you have multiple accounts. 
+##SBATCH --account=VLSCI    
+
+module load namd-xl-pami-smp/2.9
+
+# Note: newer versions of namd may exist.  Alter module accordingly. 
+
+
+# -Submit the job: ----------------------- 
+
+srun  --ntasks-per-node $ntpn  namd2 +ppn $ppn namd_1ubq_restart_example.conf > Namd_1ubq_restart_example_output.txt 
+
+

NAMD/2019ubiq/sbatch_namd_start_bluegene

+#!/bin/bash
+## sbatch launching script                     March 2014  m.kuiper
+##  - A script to run a simple NAMD job on the vlsci BlueGene/Q cluster, Avoca.
+
+#SBATCH --nodes=4
+ntpn=8        # number of tasks per node: 
+ppn=8         # processors per node: 
+
+## 30 minute walltime:
+#SBATCH --time=0:30:0
+
+# add your account number here if you have multiple accounts. 
+##SBATCH --account=VLSCI    
+
+module load namd-xl-pami-smp/2.9
+
+# Note: newer versions of namd may exist.  Alter module accordingly. 
+
+
+# -Submit the job: ----------------------- 
+
+srun  --ntasks-per-node $ntpn  namd2 +ppn $ppn namd_1ubq_example.conf > Namd_1ubq_example_output.txt 
+
+