From: Grace Brannigan (gracebrannigan_at_gmail.com)
Date: Thu Nov 19 2009 - 14:06:53 CST
This can all be done in one job. First of all, there is no need to make the
pdb from the dcd, unless I'm misunderstanding what you're doing. NAMD can
create a restart file for you, in either binary or text format. The
extension is .coor, but it takes the place of a pdb with NAMD. Secondly, you
can have two commands in the NAMD config, such as
minimize 100
run 250000
If you want to change the constraints between minimize and run, you can use
the constraintscaling parameter (assuming you are not changing the atoms you
are applying the constraints to but simply scaling them down uniformly.)
i.e.
constraintscaling 1.0
minimize 100
constraintscaling 0.0
run 250000
Hope this helps,
Grace
On Thu, Nov 19, 2009 at 12:55 PM, Richard Owczarzy <rowczarzy_at_idtdna.com>wrote:
> 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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