From: Ivan Gregoretti (ivangreg_at_gmail.com)
Date: Thu Jun 26 2014 - 08:34:16 CDT
Thank you Shailesh.
Complex, working, comprehensive examples like yours are what I was
looking for when I first joined the list.
Ivan
On Thu, Jun 26, 2014 at 5:41 AM, Shailesh Pandey <shaileshp51_at_gmail.com> wrote:
> Thank you very much friends,
>
> I tried solution suggested by Norman Giest, and it worked for me after
> little tweaking, I think scripts which worked for me might be useful to some
> other users, willing to do some thing similar.
>
> I have used PBS queuing system, and PBS job submission script as well as
> script for namd-run are here.
>
> ##############################
> NAMD-SCRIPT-STARTS-HERE###########################################
> #!/bin/bash
> base_file_name="rCplx01_C" ;# Prefix for namd outputfiles
> molecule_name="prot_pep_cplx" ;# Prefix of pdb/psf files if it
> is abc.psf/abc.pdb then here "abc"
>
> simulation_time=52 ;# Simulation length in (
> ps / ns ) unit as per "steps_unit_time"
> sim_restart_time=10
> equilibration_time=2
>
> steps_unit_ns=1000000
> steps_unit_ps=1000
>
> restart_freq=$((500*$steps_unit_ps))
> steps_unit_time=$(($steps_unit_ns))
>
> restart_counts=$(( ($simulation_time + $sim_restart_time -
> $equilibration_time + 1 ) / $sim_restart_time ))
> echo $restart_counts
>
> time_done=0
> for i in $(seq 1 $restart_counts);
> do
> i_pre=$(($i-1))
> time_left=$(($simulation_time - $time_done))
> sim_block_time=$sim_restart_time
> if [ "$sim_block_time" -gt "$time_left" ]; then
> sim_block_time=$((time_left)); fi
>
> echo $i_pre
> cat > ${base_file_name}_${i}.namd <<ENDIN
>
> #############################################################
> ## JOB DESCRIPTION ##
> #############################################################
>
> # restart of a run
> # peptide in a Water Box
> #
> # to run: namd filename.conf > filename.log &
>
> #############################################################
> ## ADJUSTABLE PARAMETERS ##
> #############################################################
>
> structure ${molecule_name}.psf
> coordinates ${molecule_name}.pdb
> set temperature 310
>
> if {${i} == 1} {
> #coordinates ${molecule_name}.pdb
> set block_run_time $(($equilibration_time))
> set rs 0
> set rsMin 1
> set firsttimestep 0
> } else {
> set block_run_time $(($sim_block_time))
> set rs 1
> set rsMin 0
> set inputname ${base_file_name}_${i_pre}
> set firsttimestep [ expr { $time_done * $steps_unit_time } ]
> }
>
> set outputname ${base_file_name}_${i}
>
> set runsteps [ expr { \$block_run_time * $steps_unit_time} ] ;# x *
> 1ns_steps + .4ns equili
>
>
> # Continuing a job from the restart files
> # if {0} is true
> # set rs 0 ;# use restart file? 1 = yes
> # set rsMin 1 ;# do mininmize? 0=No, 1=yes or 2 if velocities .vel
> not provided
> if {\$rs==1} {
> binCoordinates \$inputname.coor
> binVelocities \$inputname.vel ;# remove the "temperature" entry if
> you use this!
> extendedSystem \$inputname.xsc
> }
> # Continuing a job but not from restart files
> if {\$rs==2} {
> binCoordinates \$inputname.coor
> # binVelocities \$inputname.vel ;# remove the "temperature" entry if
> you use this!
> extendedSystem \$inputname.xsc
> }
>
>
> #############################################################
> ## SIMULATION PARAMETERS ##
> #############################################################
> # Input
> paraTypeCharmm on
> parameters ../../par_all27_prot_lipid.inp
>
> # NOTE: Do not set the initial velocity temperature if you
> # have also specified a .vel restart file!
> # temperature $temperature
> # keep temp if want to assign new velocitites
>
>
> # Periodic Boundary conditions
> # NOTE: Do not set the periodic cell basis if you have also
> # specified an .xsc restart file!
> if {\$rs==0} {
> # you get the info to make the following from:
> # set sel [atomselect top all]
> # cell basis vectors:
> # measure minmax $sel # then take the difference
> # cellOrigin:
> # measure center $sel
> #
>
> cellBasisVector1 64.89 0. 0.0
> cellBasisVector2 0.0 82.20 0.0
> cellBasisVector3 0.0 0.0 65.90
> cellOrigin 2.88 -26.92 -42.18
> }
> wrapWater on
> wrapAll on
>
>
>
> # Force-Field Parameters
> exclude scaled1-4
> 1-4scaling 1.0
> cutoff 12.
> switching on
> switchdist 10.
> pairlistdist 13.5
>
>
> # Integrator Parameters
> timestep 1.0 ;# 2fs/step
> rigidBonds water ;# needed for 2fs steps
> nonbondedFreq 1
> fullElectFrequency 2
> stepspercycle 50
>
>
> #PME (for full-system periodic electrostatics)
> if {1} {
> PME yes
> PMEGridSpacing 1.0
>
> PMEGridSizeX 72
> PMEGridSizeY 84
> PMEGridSizeZ 72
> }
>
> # Constant Temperature Control
> if {\$rs==0} {
> temperature \$temperature ;# if velocity file is used on restart
> disable this
> }
>
> langevin on ;# do langevin dynamics
> langevinDamping 1 ;# damping coefficient (gamma) of 1/ps
> langevinTemp \$temperature
> langevinHydrogen no ;# don't couple langevin bath to hydrogens
>
>
> # Constant Pressure Control (variable volume)
> if {1} {
> useGroupPressure yes ;# needed for 2fs steps
> useFlexibleCell no ;# no for water box, yes for membrane
> useConstantArea no ;# no for water box, yes for membrane
>
> langevinPiston on
> langevinPistonTarget 1.01325 ;# in bar -> 1 atm
> langevinPistonPeriod 100.
> langevinPistonDecay 50.
> langevinPistonTemp \$temperature
> }
>
>
> # Output Parameters
> outputname \$outputname
> firsttimestep \$firsttimestep
>
> restartfreq $restart_freq ;# 500000steps = every 500ps
> dcdfreq 200
> xstFreq 200
> outputEnergies 200
> outputPressure 200
>
>
> # Fixed Atoms Constraint (set PDB beta-column to 1)
> if {0} {
> fixedAtoms on
> fixedAtomsFile myfixedatoms.pdb
> fixedAtomsCol B
> }
>
>
> # IMD Settings (can view sim in VMD)
> if {0} {
> IMDon on
> IMDport 3000 ;# port number (enter it in VMD)
> IMDfreq 1 ;# send every 1 frame
> IMDwait no ;# wait for VMD to connect before running?
> }
>
>
> #############################################################
> ## EXTRA PARAMETERS ##
> #############################################################
>
> # Put here any custom parameters that are specific to
> # this job (e.g., SMD, TclForces, etc...)
>
> #############################################################
> ## EXECUTION SCRIPT ##
> #############################################################
>
> # Minimization
> if {\$rsMin==1} {
> minimize 2000
> reinitvels \$temperature ;# the temperature statement above
> verforms vel reassignment
> }
>
> run \$runsteps
>
> ENDIN
>
> echo "$1,$2: is namd2 run with arguments"
> cmd="$1 ${base_file_name}_${i}.namd "
> echo $cmd
> $cmd
>
> if [ "$i" -eq "1" ]; then time_done=$(($time_done + $equilibration_time));
> else time_done=$(($time_done + $sim_block_time)); fi
> done
>
> ############################## NAMD-SCRIPT-ENDS-HERE###################
>
> save it in a file with name "namd_runCplx01.sh" in directory
> "absolute/path/to/current/namd-job"
>
>
> ############################## PBS-JOB-SUBMISSION-SCRIPT-STARTS-HERE
> ##############
>
> #! /bin/bash
> #PBS -l nodes=2:ppn=8
> #PBS -l walltime=100:00:00
> #PBS -N myjobname
> #PBS -q myquename
> #PBS -r n
> #PBS -V
> #PBS -o o.$PBS_JOBID
> #PBS -e e.$PBS_JOBID
>
>
> export I_MPI_JOB_CONTEXT=$PBS_JOBID
> export I_MPI_FABRICS=shm:ofa
> export I_MPI_OFA_ADAPTER_NAME=mlx4_0
>
> echo PBS JOB id is $PBS_JOBID
> echo PBS_NODEFILE is $PBS_NODEFILE
> echo PBS_QUEUE is $PBS_QUEUE
> NPROCS=`wc -l < $PBS_NODEFILE`
> NRINGS=`wc -l < $PBS_NODEFILE`
> NRINGS=`cat $PBS_NODEFILE|sort|uniq|wc -l`
>
>
> echo NPROCS is $NPROCS
>
> outdir="absolute/path/to/current/namd-job"
> cd $outdir
>
> cat $PBS_NODEFILE > pbsnodes
> export rsh=/usr/bin/ssh
>
> progdir="$HOME/NAMD_2.9_Linux-x86_64-ibverbs"
>
> nodefile=namd6.nodelist
> echo group main ++shell /usr/bin/ssh > $nodefile
> awk '{ for (i=0;i<1;++i) {print "host",$1} }' pbsnodes>>$nodefile
>
> mpdboot --totalnum=$NRINGS --file=$PBS_NODEFILE --rsh=/usr/bin/ssh
> --verbose --ordered
> $outdir/namd_runCplx01.sh "$progdir/charmrun ++mpiexec +p$NPROCS
> $progdir/namd2 " > ${outdir}/l.$PBS_JOBID.log
> mpdallexit
> exit 0
>
>
> ############################## PBS-JOB-SUBMISSION-SCRIPT-ENDS-HERE
> ##############
>
>
> give execute permission to file
> "absolute/path/to/current/namd-job/namd_runCplx01.sh"
>
> and use PBS script for job submission
>
> On Tue, Jun 10, 2014 at 1:15 PM, Ajasja Ljubetič <ajasja.ljubetic_at_gmail.com>
> wrote:
>>
>> Hi!
>>
>> I usually write a bash shell script that calls namd with the right
>> parameters so that I get 1 ns long DCD files. Environment variables can be
>> accessed using
>> $env(NAME_OF_VARIABLE) inside of the NAMD configuration file (I'm
>> attaching an example).
>>
>> The other option is if you can use the colvars module to do your analysis
>> on the fly, while the simulation is running.
>>
>> Good luck,
>> Ajasja
>>
>>
>>
>>
>>
>> On 9 June 2014 19:54, Shailesh Pandey <shaileshp51_at_gmail.com> wrote:
>>>
>>> Dear NAMD users,
>>>
>>> I am running NAMD simulations, but my problem is that users are allowed
>>> to store only limited data (say 100GB) in their account at our computing
>>> center, but when i run a simulations of 100ns allocated user space gets
>>> filled and simulation is killed by scheduler before completing. I want to
>>> simulations of 100ns length because jobs usually wait for weeks in queue
>>> only after such long wait get chance to run, So I want when I get chance to
>>> run i should run 100ns in one chance.
>>>
>>>
>>> I want to write different DCD for every (say 20ns) so that once
>>> simulation crosses 20 ns, it should start writing to different DCD file and
>>> after backing up earlier one I can safely delete older DCD without affecting
>>> running simulation.
>>>
>>> Eg. setting restartsave yes we can save restart files for every restart
>>> timestep, A similar thing i want for DCD file.
>>>
>>> I can not increase DCDfreq, because frames are need for analysis.
>>>
>>> Any help is appreciated thank you.
>>
>>
>
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