From: Giacomo Fiorin (giacomo.fiorin_at_gmail.com)
Date: Tue May 16 2017 - 09:39:59 CDT
Hi Vlad, I just fixed the error is fixed here:
https://github.com/colvars/colvars/commit/fd7445328d5f670863690869bf9571
6dce8a1dd8
Thanks you for reporting it.
Giacomo
On Tue, May 16, 2017 at 10:08 AM, Jérôme Hénin <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>
> 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 <+49%20251%2070365324>; Fax: +49-251-70365-399
>> <+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
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