Re: Simultaneous water and protein minimization

From: jkmann_at_buffalo.edu
Date: Thu Nov 19 2009 - 15:07:54 CST

I do use both minimize and run together in configuration file.In my last email,
configuration file didn't come up complete so I'm sending them in attachment.
In my first step I do water minimization and keep the coordinates of protein fix.
I exit my conf file before Run because i just want to equilibrate water around
the protein.
In second step, I do protein minimization and dynamics.I turn off the fixed atoms
and change coordinate pdb file.

You are correct that I do not need to make new pdb as .coor file store the
coordinates.But my concern is how in single configuration file,
first coordinates are read from the input given intially,
then after water minimize 1000, coordinates are read from .coor file and fixed
atoms are turned off
then protein minimize 1000 and Run 2000000.
Any suggestion will be highly appreciated.

Thanks for helping.

On Thu 11/19/09 3:06 PM , Grace Brannigan gracebrannigan_at_gmail.com sent:
> 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 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
> [2]
> 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: [mailto:]
> 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: [owne
> > ] 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
> >
> >
> >
> >
> >
> >
> >
> >
> >
>
>
> Links:
> ------
> [2] http://www.injunea.demon.co.uk/pages/page203.htm
>
>


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