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

From: Vlad Cojocaru (vlad.cojocaru_at_mpi-muenster.mpg.de)
Date: Tue May 16 2017 - 10:50:10 CDT

Thanks Giacomo,

Any idea when this should make it to the NAMD nightly builds ?

Cheers
Vlad

On 05/16/2017 04:39 PM, Giacomo Fiorin wrote:
> Hi Vlad, I just fixed the error is fixed here:
> https://github.com/colvars/colvars/commit/fd7445328d5f670863690869bf95716dce8a1dd8
> <https://github.com/colvars/colvars/commit/fd7445328d5f670863690869bf95716dce8a1dd8>
>
> Thanks you for reporting it.
>
> Giacomo
>
> On Tue, May 16, 2017 at 10:08 AM, Jérôme Hénin <jerome.henin_at_ibpc.fr
> <mailto:jerome.henin_at_ibpc.fr>> 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
> <https://urldefense.proofpoint.com/v2/url?u=https-3A__github.com_colvars_colvars_issues_118&d=DwMFaQ&c=8hUWFZcy2Z-Za5rBPlktOQ&r=6cQ04kjNHUuxT8SDe1wb0TtPDsnWRp4T4iwoYRLFpsY&m=5ox-4AZPajCsXBpGUt65Ufg0fpmKUsB_Ikn-xKQNdSQ&s=IvVxSAUBZzWS2eh7RuM8ASxL4QMYrwzvzf9RTUSXkNY&e=>
>
> 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 <tel:+49%20251%2070365324>; Fax:
> +49-251-70365-399 <tel:+49%20251%2070365399>
> Email: vlad.cojocaru[at]mpi-muenster.mpg.de
> <https://urldefense.proofpoint.com/v2/url?u=http-3A__mpi-2Dmuenster.mpg.de&d=DwMFaQ&c=8hUWFZcy2Z-Za5rBPlktOQ&r=6cQ04kjNHUuxT8SDe1wb0TtPDsnWRp4T4iwoYRLFpsY&m=5ox-4AZPajCsXBpGUt65Ufg0fpmKUsB_Ikn-xKQNdSQ&s=QTIw-Vm9dLSQ4jFG_HzTs4gg8RRxNhm5T6d-OV9_80c&e=>
> http://www.mpi-muenster.mpg.de/43241/cojocaru
> <https://urldefense.proofpoint.com/v2/url?u=http-3A__www.mpi-2Dmuenster.mpg.de_43241_cojocaru&d=DwMFaQ&c=8hUWFZcy2Z-Za5rBPlktOQ&r=6cQ04kjNHUuxT8SDe1wb0TtPDsnWRp4T4iwoYRLFpsY&m=5ox-4AZPajCsXBpGUt65Ufg0fpmKUsB_Ikn-xKQNdSQ&s=wNjaY9EYL5X7YgITAEY7_AWUbSprtkIX1aV9mEF8r7A&e=>
>
>
>
>
>
> --
> Giacomo Fiorin
> Associate Professor of Research, Temple University, Philadelphia, PA
> Contractor, National Institutes of Health, Bethesda, MD
> http://goo.gl/Q3TBQU
> https://github.com/giacomofiorin <https://github.com/giacomofiorin>

-- 
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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