Re: scriptedColvarForces doesn't work in recent NAMD builds

From: Jérôme Hénin (jerome.henin_at_ibpc.fr)
Date: Wed Apr 11 2018 - 12:12:26 CDT

Thanks Jeff, I see what the problem is. I think a workaround for now is to
specify the wall potentials of your colvars as a separate instance of
harmonicWalls bias, and remove the upper/lowerWall keywords.

This should be an easy fix, but I can't do it right away.

Best,
Jerome

On 11 April 2018 at 18:51, Jeff Comer <jeffcomer_at_gmail.com> wrote:

> Thanks, Jerome. I've attached an example system. Running NAMD 2.12 on
> "test_funnel_amber.0.namd" gives log file output from
> calc_colvar_forces, while running recent NAMD builds on it do not.
> Maybe I am doing something unusual?
>
> Jeff
>
> –––––––––––––––––––––––––––––––––––———————
> Jeffrey Comer, PhD
> Assistant Professor
> Institute of Computational Comparative Medicine
> Nanotechnology Innovation Center of Kansas State
> Kansas State University
> Office: P-213 Mosier Hall
> Phone: 785-532-6311
> Website: http://jeffcomer.us
>
>
> On Wed, Apr 11, 2018 at 11:26 AM, Jérôme Hénin <jerome.henin_at_ibpc.fr>
> wrote:
> > Hi Jeff,
> >
> > This is the first report I see of such an issue. I have just tested it
> with
> > both NAMD 2.12 and a recent build, so it must be a more specific problem.
> > Can you send your NAMD and colvars input?
> >
> > Thanks,
> > Jerome
> >
> > On 11 April 2018 at 18:04, Jeff Comer <jeffcomer_at_gmail.com> wrote:
> >>
> >> I'm not sure whether this is a Colvars problem or a NAMD problem.
> >>
> >> My Colvars configuration file includes "scriptedColvarForces on". In
> >> my NAMD configuration file, I have defined the proc calc_colvar_forces
> >> to print some information to the log file and apply a restraint
> >> force. Using NAMD_2.12 (multcore or multicore CUDA), this works fine.
> >> The status information is written to the log file and the effects of
> >> the force are clearly seen in the trajectory. For recent NAMD builds,
> >> for example, NAMD_Git-2018-04-06_Linux-x86_64-multicore, no
> >> information from calc_colvar_forces appears in the log file and the
> >> force is not applied.
> >>
> >> I looked in the Colvars GitHub, but didn't find a clear reference to
> >> this issue. Is this something I can fix by recompiling NAMD with a
> >> newer Colvars version? Is there a work-around?
> >>
> >> Thanks!
> >> Jeff
> >>
> >> –––––––––––––––––––––––––––––––––––———————
> >> Jeffrey Comer, PhD
> >> Assistant Professor
> >> Institute of Computational Comparative Medicine
> >> Nanotechnology Innovation Center of Kansas State
> >> Kansas State University
> >> Office: P-213 Mosier Hall
> >> Phone: 785-532-6311
> >> Website: http://jeffcomer.us
> >>
> >
>

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