From: Vlad Cojocaru (vlad.cojocaru_at_mpi-muenster.mpg.de)
Date: Tue May 16 2017 - 09:36:38 CDT
Thanks Jerome,
I will try the "scalable off" option
Best, Vlad
On 05/16/2017 04:08 PM, Jérôme Hénin wrote:
> Hi Vlad,
>
> Thanks a lot for your report. I have identified the problem and
> created an issue in our tracker:
> https://github.com/colvars/colvars/issues/118
>
> The distanceInv function is wrongly identified as depending only on
> the groups' centers of mass.
>
> As a workaround until it gets fixed, you can specify "scalable off"
> within the distanceInv block.
>
> Best,
> Jerome
>
> On 16 May 2017 at 15:20, Vlad Cojocaru
> <vlad.cojocaru_at_mpi-muenster.mpg.de
> <mailto:vlad.cojocaru_at_mpi-muenster.mpg.de>> wrote:
>
> I should add here that NAMD 2.11 also performs the simulation
> correctly. This is really an NAMD-2.12 specific bug ...
>
> Best
> Vlad
>
>
> On 05/15/2017 11:18 AM, Vlad Cojocaru wrote:
>
> Dear all,
>
> I am seeing a problem specific to NAMD 2.12. When applying a
> harmonic restraint (test steered MD simulation) on a
> "distanceInv" collective variable, the variable is not changed
> during the simulation (despite of targetCenters set to 40,
> the colvar stays around its initial value (6.8-7.2) throughout
> the simulation, see configuration file below). Exactly the
> same test simulation runs absolutely fine with NAMD 2.10
> (currently I am testing with 2.11 as well).
>
> The regular "distance" colvar works fine. Has anybody else
> experienced this ?
>
> If you need further information/files off the list please let
> me know
>
> Best wishes
> Vlad
>
>
> colvarsTrajFrequency 100
>
> colvar {
> name DistInv-PouS
> width 0.5
> distanceInv {
> exponent 10
> group1 {
> atomsFile colvar_ref.pdb
> atomsCol B
> atomsColValue 1.0
> }
> group2 {
> atomsFile colvar_ref.pdb
> atomsCol B
> atomsColValue 3.0
> }
>
> }
>
> }
>
> colvar {
> name DistInv-PouHD
> width 0.5
> distanceInv {
> exponent 10
> group1 {
> atomsFile colvar_ref.pdb
> atomsCol B
> atomsColValue 2.0
> }
> group2 {
> atomsFile colvar_ref.pdb
> atomsCol B
> atomsColValue 4.0
> }
>
> }
>
> }
>
>
> harmonic {
> colvars DistInv-PouS
> centers 5
> targetCenters 40
> targetNumSteps 10000
> outputCenters on
> outputAccumulatedWork on
> forceConstant 10.0
> }
>
>
>
>
> --
> Vlad Cojocaru, Ph.D., Project Group Leader
> Department of Cell and Developmental Biology
> Max Planck Institute for Molecular Biomedicine
> Röntgenstrasse 20, 48149 Münster, Germany
> Tel: +49-251-70365-324; Fax: +49-251-70365-399
> Email: vlad.cojocaru[at]mpi-muenster.mpg.de
> <http://mpi-muenster.mpg.de>
> http://www.mpi-muenster.mpg.de/43241/cojocaru
> <http://www.mpi-muenster.mpg.de/43241/cojocaru>
>
>
-- Vlad Cojocaru, Ph.D., Project Group Leader Department of Cell and Developmental Biology Max Planck Institute for Molecular Biomedicine Röntgenstrasse 20, 48149 Münster, Germany Tel: +49-251-70365-324; Fax: +49-251-70365-399 Email: vlad.cojocaru[at]mpi-muenster.mpg.de http://www.mpi-muenster.mpg.de/43241/cojocaru
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