Re: Colvar not working in NAMD2.12 Linux version

From: Jérôme Hénin (jerome.henin_at_ibpc.fr)
Date: Thu Mar 21 2019 - 09:32:30 CDT

Dear Mukta,

This is due to the special way NAMD parses its config file, which is both a
set of key-value lines, and a Tcl script. After the first "minimize" or
"run" command, it switches to "Tcl-only" mode which is too late to setup
the Colvars module.

The solution is to move the "colvars on" line to earlier in your script,
before the first "minimize" or "run" command. Then load your Colvars
configuration with "cv configfile <filename>", whenever needed.

Best,
Jerome

On Thu, 21 Mar 2019 at 00:05, Mukta Sharma <sharmamukta.924_at_gmail.com>
wrote:

> Dear NAMD users,
> On running the colvar, I am getting the following error message:
> CL: Setting parameter colvars to on
> FATAL ERROR: Setting parameter colvars from script failed!
> ------------- Processor 3 Exiting: Called CmiAbort ------------
> Reason: FATAL ERROR: Setting parameter colvars from script failed!
> *On running it locally:*
> ------------ Processor 0 Exiting: Called CmiAbort ------------
> Reason: FATAL ERROR: Error in the collective variables module: exiting.
> FATAL ERROR: Error in the collective variables module: exiting.
> Charm++ fatal error:
> FATAL ERROR: Error in the collective variables module: exiting.
> T*he atom number in group 1 and 2 are the same and I want to see how
> close atoms in group 1 are coming to atoms of group 2 which are different
> in both groups. The colvar file I am using for the run is:*
> # collective variables config file: two distances
> colvarsTrajFrequency 100 # output values every 100 steps
> colvar {
> name 1st-colvar # needed to identify the variable
> outputSystemForce yes # report also the system force on this colvar
> # (in addition to the current value)
> distance {
> group1 {
> atomNumbers 4924
> }
> group2 {
> atomNumbers 1913 1934
> }
> }
> }
> colvar {
> name 2nd-colvar
> outputSystemForce yes # report also the system force on this colvar
> # (in addition to the current value)
> distance {
> group1 {
> atomNumbers 4924
> }
> group2 {
> atomNumbers 1731 1752
> }
> }
> }
> harmonic {
> name my_pot
> colvars 1st-colvar 2nd-colvar
> centers 0.0 0.0
> forceConstant 1.0
> }
> Thanks in anticipation.
>

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