AW: Large number of simulations in parallel using replica exchange.

From: Norman Geist (norman.geist_at_uni-greifswald.de)
Date: Tue Feb 12 2019 - 01:54:14 CST

You can identify the respective replica by its replica id to set your parameters as desired. Have a look at the remd example shipped with the source.

 

Von: owner-namd-l_at_ks.uiuc.edu [mailto:owner-namd-l_at_ks.uiuc.edu] Im Auftrag von Dipak Balasaheb Sanap
Gesendet: Montag, 11. Februar 2019 21:52
An: namd-l_at_ks.uiuc.edu
Betreff: namd-l: Large number of simulations in parallel using replica exchange.

 

Hi, I have a simple problem. I need to run large number of short simulations in parallel for different systems. And, my conf file has all the parameters same except structure, coordinates, parameters and outputname. I am planning to use replica exchange with no communication among replicas so I can run all of the simulations in single command. Something like this, namd2 replica.conf +replicas 6000 which uses just exchanges variable parameters and run 6000 simulations in parallel. My question is, how can I write replica.conf file to switch the parameters. Below is my normal conf file for a single simulation and I have commented where I need to switch the variable (variable 1,2,3 and 4). I am aware that I need to use myReplica function or something like that. Thank you very much.

##########################################################
#ADJUSTABLE PARAMETERS ##
#############################################################

# Variable 1 and 2, use different psf and pdb file for every replica

structure input/cg_20_22_psfgen.psf
coordinates input/cg_20_22_psfgen.pdb

 

set temperature 310

#Variable 3, choose output directory for every replica

set outputname output/iteration1_0.6

 

firsttimestep 0
#############################################################
## SIMULATION PARAMETERS ##
#############################################################
# Input
paraTypeCharmm on

#Variable 4, change parameter file for every replica.

parameters input/from-aa_20_22_0.6.par

 

temperature $temperature
# Force-Field Parameters
exclude 1-2
cutoff 30.0
switching on
switchdist 20.0
pairlistdist 100.0
hgroupcutoff 0
# Integrator Parameters
timestep 100.0
nonbondedFreq 1
stepspercycle 20
dielectric 20
# Constant Temperature Control
langevin on
langevinDamping 2.0
langevinTemp $temperature
langevinHydrogen off
# Output
outputName $outputname
restartfreq 400
dcdfreq 1000
xstFreq 400
outputEnergies 400
outputPressure 400
#############################################################
## EXECUTION SCRIPT ##
#############################################################
# Minimization
minimize 2000
reinitvels $temperature
 run 100000

 

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