colvars.traj file empty

From: Ashutosh Shandilya (
Date: Thu Nov 18 2021 - 19:40:50 CST

Dear Users,
I am running abf simulation with namd and it seems to be running fine
generating pmf and gradient files, but colvavrs.traj file is empty.
Although output logfile says

colvars: This version was built with the C++11 standard or higher.
colvars: Using NAMD interface, version "2019-12-04".
colvars: The restart output state file will be
colvars: The final output state file will be "prod9.colvars.state".
colvars: Writing to colvar trajectory file "prod9.colvars.traj".
but they are empty.

My abf input files looks like this

 colvar {
                 width 0.05
                lowerboundary 0
                upperboundary 1
                extendedlagrangian on
                extendedfluctuation 0.05
                  gspath {
               atoms {atomnumbers { 12961 12975 ..... 61848 61880 }}
                refPositionsFile1 1.pdb
                refPositionsFile2 2.pdb
                refPositionsFile3 3.pdb
                refPositionsFile102 102.pdb
                refPositionsFile103 103.pdb
                refPositionsFile104 104.pdb
                refPositionsFile105 105.pdb
                refPositionsFile106 106.pdb
                refPositionsFile107 107.pdb
                refPositionsFile108 108.pdb
                abf {
                        colvars gs
                        fullSamples 500
                        historyfreq 1000

Conf file inputs:
# output
outputname ${runnew}
outputenergies 500
outputtiming 500
binaryoutput no
restartfreq 500
dcdfreq 1000
dcdfile ${runnew}.dcd
wrapall off
wrapNearest on

# for restarting:
restartname ${runnew}-restart
colvars on
cv configfile input_file.tcl
run $step

Kindly suggest,

This archive was generated by hypermail 2.1.6 : Fri Dec 31 2021 - 23:17:12 CST