AW: Multiple Runs in a Single Conf File

From: Norman Geist (norman.geist_at_uni-greifswald.de)
Date: Wed Jun 08 2011 - 03:27:54 CDT

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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