Re: colvar distanceInv not propagated with a harmonic moving restraint in NAMD 2.12

From: Jérôme Hénin (jerome.henin_at_ibpc.fr)
Date: Tue May 16 2017 - 09:08:46 CDT

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>
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://www.mpi-muenster.mpg.de/43241/cojocaru
>
>

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