From: jkmann_at_buffalo.edu
Date: Thu Nov 19 2009 - 11:04:17 CST
----- Original Message -----
From: jkmann_at_buffalo.edu
To: "Richard Owczarzy" rowczarzy_at_idtdna.com
Sent: Thu 11/19/09 12:02 PM
Subject: Fwd: 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
>
>
>
>
>
>
>
>
>
This archive was generated by hypermail 2.1.6 : Wed Feb 29 2012 - 15:53:31 CST