From: Richard Owczarzy (rowczarzy_at_idtdna.com)
Date: Thu Nov 19 2009 - 11:55:08 CST
What command are you submitting to teragrid? Is it NAMD command, e.g.
something like namd +p2 run.conf >run.out ? (run.conf is your NAMD
configuration file, etc.)
What operating system is teragrid running? I assumed that your OS is
some version of LINUX/UNIX. Instead of submitting one NAMD command, you
submit to teragrid a UNIX shell script written in one plain text file,
e.g.
$HOME/myscript.sh
The file myscript.sh will contain all commands for your three steps:
#!/bin/bash
NAMD.... (running 1st minimization)
.. (running script to create pdb)
NAMD.... (running 2nd molecular dynamics)
The idea is to run all NAMD commands in one batch job (myscript.sh).
If you google "script bash linux", you will get tons of info.
For example, see http://www.injunea.demon.co.uk/pages/page203.htm
In LINUX/UNIX, there are different versions of shells, you pick one that
you have installed.
Make sure that your script file (myscript.sh) has executable permission,
i.e. execute this: chmod +x myscript.sh
I hope this helps.
Richard
-----Original Message-----
From: jkmann_at_buffalo.edu [mailto:jkmann_at_buffalo.edu]
Sent: Thursday, November 19, 2009 11:03 AM
To: Richard Owczarzy
Subject: RE: namd-l: Simultaneous water and protein minimization
Yes i use following script to create pdb for further protein
minimization.
set fname "swemt"
mol new ${fname}_ion.pdb
mol addfile ${fname}.dcd waitfor all
set a [atomselect top "all" frame 2]
$a writepdb ${fname}_min.pdb
But doing this I have to retrieve pdb after water minimization and also
have to
make changes in NAMD configuration file, after this I resubmit my job to
teragrid
which puts me up in long Queue.
NAMD script for water minimization:
structure swemt_ion.psf
#COORDINATES SWEMT_MIN.PDB
coordinates swemt_ion.pdb
set temperature 310
set outputname swemt
set inputname swemt
#binCoordinates $inputname.coor
#binvelocities $inputname.vel
#extendedSystem $inputname.xsc
firsttimestep 0
#############################################################
## SIMULATION PARAMETERS ##
#############################################################
# Input
paraTypeCharmm on
parameters /san/user/MD/toppar/par_all27_prot_lipid.inp
parameters /san/user/MD/toppar/complex.parm
temperature $temperature
# Force-Field Parameters
exclude scaled1-4
1-4scaling 1.0
cutoff 12.
switching on
switchdist 10.
pairlistdist 13.5
# Integrator Parameters
timestep 1.0
rigidBonds all
#rigidBonds none
nonbondedFreq 1
fullElectFrequency 2
stepspercycle 10
# Constant Temperature Control
if (1) {
langevin on ;# do langevin dynamics
langevinDamping 5 ;# damping coefficient (gamma) of 5/ps
langevinTemp $temperature
langevinHydrogen off ;# don't couple langevin bath to hydrogens
# Periodic Boundary Conditions
cellBasisVector1 75.1879997254 0. 0.
cellBasisVector2 0. 55.4099998474 0.
cellBasisVector3 0. 0. 58.8969993591
cellOrigin 19.1018161774 -15.0435552597 24.6389865875
wrapAll on
# PME (for full-system periodic electrostatics)
PME yes
PMEGridSizeX 81
PMEGridSizeY 64
PMEGridSizeZ 64
}
# Constant Pressure Control (variable volume)
if (1) {
useGroupPressure yes ;# needed for rigidBonds
useFlexibleCell no
useConstantArea no
langevinPiston on
langevinPistonTarget 1.01325 ;# in bar -> 1 atm
langevinPistonPeriod 100.
langevinPistonDecay 50.
langevinPistonTemp $temperature
}
# Output
outputName $outputname
restartfreq 2500 ;# 500steps = every 1ps
dcdfreq 2500
xstFreq 2500
outputEnergies 2500
outputPressure 2500
#############################################################
## EXTRA PARAMETERS ##
#############################################################
FIXEDATOMS YES
FIXEDATOMSCOL B
FIXEDATOMSFILE SWEMT_FIXED.PDB
#
#############################################################
## EXECUTION SCRIPT ##
#############################################################
# Minimization
minimize 5000
exit
FOR {SET T 1} {$T Can you have a LINUX/UNIX script that runs one
simulation after
> another?Can you submit the script instead of NAMD to the cluster?
>
> Richard
>
> -----Original Message-----
> From: owner-namd-l_at_ks.uiuc.edu [owne
> r-namd-l_at_ks.uiuc.edu] OnBehalf Of jkmann_at_buf
> falo.eduSent: Wednesday, November 18, 2009 3:58 PM
> To: namd-l_at_ks.
> uiuc.eduSubject: namd-l: Simultaneous water and protein minimization
>
>
> Hi everyone,
>
> When I do simulation for protein, I first solvate my protein and fix
> itscoordinate and submit the job for water minimization.Then I
retrieve
> thedcd
> file, load it to the existing pdb file and save pdb with coordinates
> from last
> frame of dcd trajectory.
> Now I use the coordinates of this pdb in the NAMD configuration file
to
> do
> protein minimization.So, its a kind of two step process but as I do my
> job
> submission to some outside cluster, everytime I have to bring back the
> structure
> to my CPU and then again load to the outside system which again puts
me
> to long
> Queue. To avoid this I'm trying to modify my configuration file such
> that it
> first takes the coordinates from fixed pdb and do water minimization
> andproceeding that take coordinate from water minimized structure to
do
> further
> dynamics, all in one step. Has anyone tried this before or is it just
> impossible?
> I'm trying to use some if else commands but NAMD doesn't recognize
> thesecommands.
> I hope my question is understandable and any help will be appreciated.
>
> Thank you
>
>
>
>
>
>
>
>
>
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