From: Vlad Cojocaru (vlad.cojocaru_at_mpi-muenster.mpg.de)
Date: Tue May 16 2017 - 08:20:31 CDT
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://www.mpi-muenster.mpg.de/43241/cojocaru
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