From: Giacomo Fiorin (giacomo.fiorin_at_gmail.com)
Date: Thu Nov 18 2021 - 21:05:07 CST
Could be buffering.
Try "run 0" or a small number of steps.
On Thu, Nov 18, 2021 at 8:42 PM Ashutosh Shandilya <scfbioiitd_at_gmail.com>
wrote:
> 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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