Restart multiple walker ABF

From: Atanu Maity (
Date: Thu May 19 2016 - 03:32:24 CDT

Dear users,

I am facing this problem while trying to restart an REMD (multiple walker)
run as a part of ABF simulation. I start the simulation using the following
command line –

mpirun -np 32 namd2 +replicas 4 abf-replica.namd +stdout
replica4/%d/job4.%d.log &

Four replicas were running using 8 core each properly.

The input contains the following lines –

structure step5_assembly.xplor_ext.psf

coordinates step5_assembly.pdb

set temp 303.15;

set outputname replica4/abf-22-prod2.[myReplica]

set inputname abf-22-prod1.1

binCoordinates $inputname.coor

binVelocities $inputname.vel

extendedSystem $inputname.xsc

outputname $outputname

restartfreq 10000;

dcdfreq 2000;

dcdUnitCell yes;

xstFreq 10000;

outputEnergies 10000;

outputTiming 10000;

# Force-Field Parameters

paraTypeCharmm on;

parameters toppar-namd/par_all36_prot.prm;

parameters toppar-namd/par_all36_lipid.prm;

parameters toppar-namd/toppar_all36_lipid_cholesterol.str;

parameters toppar-namd/toppar_all36_lipid_glycolipid.str;

parameters toppar-namd/toppar_all36_lipid_bacterial.str;

# These are specified by CHARMM

exclude scaled1-4

langevinPistonTemp $temp;

# Constant Temperature Control

langevin on; # langevin dynamics

langevinDamping 1.0; # damping coefficient of 1/ps (keep

langevinTemp $temp; # random noise at this level

langevinHydrogen off; # don't couple bath to hydrogens

colvars on


## Replica Exchange ##

##SElectionRules will be applied at each 100 steps###

source /apps/NAMD_2.11b1_Source/lib/selectionRules.tcl

source /apps/NAMD_2.11b1_Source/lib/resampleWalkers.tcl

source /apps/NAMD_2.11b1_Source/lib/minExchanges.tcl

firsttimestep 230000

replicaUniformPatchGrids on

set n 12500

set sharedFreq 100

for {set i 0} {$i < $n} {incr i} {

        run $sharedFreq

        cv bias abf1 share

        if {$i % 50 == 49} {




The problem with the restart is that I did not understand which restart
files (.coor, .vel, .state) should I use because I have four sets of such

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