From: Ashutosh Shandilya (scfbioiitd_at_gmail.com)
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
"prod9-restart.colvars.state".
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,
Thanks
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