AW: Multiple Runs in a Single Conf File

From: Norman Geist (norman.geist_at_uni-greifswald.de)
Date: Thu Jun 09 2011 - 00:40:18 CDT

Hi Rajan,

so this is not possible as it seems. But if you just use good names for your outputname and dcdfiles etc, the directory structure won't get that horrible if you run it in single runs. Also, you can do it as one batch job, which contains the writing of the configuration files and the calls to namd.

Best regards

Norman Geist.

-----Urspr√ľngliche Nachricht-----
Von: owner-namd-l_at_ks.uiuc.edu [mailto:owner-namd-l_at_ks.uiuc.edu] Im Auftrag von Rajan Vatassery
Gesendet: Mittwoch, 8. Juni 2011 16:54
An: Norman Geist
Cc: Namd Mailing List
Betreff: Re: namd-l: Multiple Runs in a Single Conf File

Norman,
        I am sorry that I did not make it clear, but I had also tried that. Of
course because it is not one of the variables that is allowed to be
passed, it did not work.
        Is it possible that the list of parameters will be expanded in future
revisions?

Thank you,

Rajan

On Wed, 2011-06-08 at 10:27 +0200, Norman Geist wrote:
> Hi,
>
> maybe try langevin on and langevin off, instead of setting the freqs to 0.
>
> Best regards
>
> Norman Geist.
>
>
> -----Urspr√ľngliche Nachricht-----
> Von: owner-namd-l_at_ks.uiuc.edu [mailto:owner-namd-l_at_ks.uiuc.edu] Im Auftrag von Rajan Vatassery
> Gesendet: Mittwoch, 8. Juni 2011 10:01
> An: namd-l_at_ks.uiuc.edu
> Betreff: namd-l: Multiple Runs in a Single Conf File
>
> Dear NAMD Users,
> I am trying to simulate a system in the following steps:
>
> 1. Minimize ~7.5k steps
> 2. Equilibrate 250k steps w 2fs/step (rigidbonds all) with a langevin
> thermostat maintaining 298 K.
> 3. Remove Langevin thermostat and run 100k more steps but with rescaling
> back to 298 K every 1k steps.
> 4. Remove rescaling and run for production run
>
> As many of you probably are guessing, when I try to change the langevin
> parameter to "off," NAMD will not let that happen. Given this section of
> the manual:
>
> http://www.ks.uiuc.edu/Research/namd/2.8/ug/node10.html ,
>
> the allowed parameters to be passed between "run" commands do not
> include the "langevin" parameter.
>
> My question: Is there a way to still keep this simulation on a single
> conf file? I have many of these to run and being able to keep one conf
> file for each test would simplify my directory structure a lot.
>
> Moreover, there are many people that are looking for a similar answer:
> http://ftp.ks.uiuc.edu/Research/namd/mailing_list/namd-l/7924.html
> http://www.ks.uiuc.edu/Research/namd/mailing_list/namd-l/8629.html
> http://www.ks.uiuc.edu/Research/namd/mailing_list/namd-l/1095.html
> http://www.ks.uiuc.edu/Research/namd/mailing_list/namd-l/12148.html
>
> These people generally have posted the error:
> FATAL ERROR: Setting parameter PARAMETER from script failed!
>
> Here is my conf file below. Thanks for your attention, and thanks to Jim
> Phillips for the answer to a previous question.
>
> Rajan Vatassery
>
>
> PS If there are any comments on the validity of my simulation, I would
> also appreciate hearing those as well (off list or on, depending on your
> preference).
>
> #############################################################
> ## JOB DESCRIPTION ##
> #############################################################
> #############################################################
> ## ADJUSTABLE PARAMETERS ##
> #############################################################
> structure ../TerthiophenePSFGEN30.psf
> coordinates Terthio30phene2p0.pdb
>
>
> set temperature 298
> set outputname MDRun30
>
> #############################################################
> ## SIMULATION PARAMETERS ##
> #############################################################
>
> # Input
> paraTypeCharmm on
> parameters 3tPhAcid_params20.prm
> temperature $temperature
>
> fixedAtoms on
> fixedAtomsCol B
>
> # Force-Field Parameters
> exclude scaled1-4
> 1-4scaling 1.0
> cutoff 16.
> switching on
> switchdist 14.
> pairlistdist 17.5
>
> # Integrator Parameters
> timestep 2.0 ;# 2fs/step
> rigidBonds all ;# needed for 2fs steps, fixes all R-H bonds
> nonbondedFreq 1
> fullElectFrequency 2
> stepspercycle 10
>
> # Constant Temperature Control
> langevin on ;# do langevin dynamics
> langevinDamping 5 ;# damping coefficient (gamma) of 5/ps
> langevinTemp $temperature
> langevinHydrogen off ;# don't couple langevin bath to hydrogens
>
>
> # Output
> outputName $outputname
>
> restartfreq 500 ;# 500steps = every 1ps
> dcdfreq 250
> xstFreq 250
> outputEnergies 100
> outputPressure 100
>
> #############################################################
> ## EXTRA PARAMETERS ##
> #############################################################
>
> #############################################################
> ## EXECUTION SCRIPT ##
> #############################################################
>
> minimize 7500 ;# if minimization not already done
>
>
> reinitvels 298 ;# start up MD equilibration
> run 250000 ;# 500 ps at 2 fs/step
>
> langevindamping 0;# turn of langevin thermostat? -- no, doesn't work
> rescaleFreq 1000
> rescaleTemp 298
>
> run 100000 ;# 200 ps
>
> #rescaleFreq 0 ;# turn off temp rescaling?
>
> run 500000 ;#
>
>
>
>
>

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