Re: namd 2.12 and plumed 2.3

From: Giacomo Fiorin (giacomo.fiorin_at_gmail.com)
Date: Tue May 02 2017 - 08:38:06 CDT

Hi Vlad, instead of dereferencing the Lattice * pointer that is part of the
SimParameters class, you should use the pointer with the same name from the
GlobalMaster class. Only the latter object is updated at each step.

Best wishes to you,

Giacomo

On Tue, May 2, 2017 at 9:12 AM, Vlad Cojocaru <vlad.cojocaru_at_mpi-muenster.mp
g.de> wrote:

> Dear all,
>
> I have managed to compile namd 2.12 with PLumed 2.3.1 support by adapting
> the patch for NAMD 2.9 to 2.12. ... We will start testing it and see if we
> encounter any problems ...
>
> Giacomo,
> Is there a way to fix the behavior in NPT simulations ? How was it fixed
> for the Colvars module ?
>
> Best wishes
> Vlad
>
>
>
>
>
> On 04/26/2017 07:01 PM, Giacomo Fiorin wrote:
>
> FYI, pay attention with NPT simulations, because in NAMD 2.9 the initial
> unit cell parameters from the configuration file were used throughout the
> simulation by all GlobalMaster objects. The outcome is that the
> minimum-image distance starts accumulating an error of the order to the box
> fluctuations.
>
> This used to be an issue for Colvars as well, but it has been fixed
> between NAMD 2.10 and 2.11, when NAMD started communicating the updated
> lattice parameters to all GlobalMaster-derived functions.
>
> Giacomo
>
> On Wed, Apr 26, 2017 at 12:43 PM, Vermaas, Joshua <Joshua.Vermaas_at_nrel.gov
> > wrote:
>
>> Take a look at the patches they distributed for 2.9. I just adapted those
>> myself for 2.11 (the line numbers where the changes take place change, but
>> the rest does not), then recompile NAMD and be happy.
>>
>> -Josh
>>
>> On 04/26/2017 10:32 AM, Vlad Cojocaru wrote:
>> Thanks ! I actually referred to running free energy simulations in
>> Plumed-enabled NAMD and not only to using the Plumed interface for analysis
>> ...
>>
>> Best wishes
>> Vlad
>>
>>
>>
>> On 04/26/2017 05:48 PM, Bassam Haddad wrote:
>> I am currently using NAMD 2.12 build (CUDA) with Plumed 2.3. I can use
>> the Plumed GUI to make certain calculations such as RMS, distance, etc.
>>
>> Though I am under the impression that in order to take full advantage of
>> colvars, and free energy calculations, you need to re-compile namd with
>> Plumed. Since I have not done this, I cannot say if it's compatible with
>> 2.12.
>>
>> Hope this helps!
>>
>> Cheers,
>> Bassam Haddad
>>
>> ---
>> Ph.D. Chemistry Portland State University
>> B.S. Biochemistry Western Washington University
>>
>> On Wed, Apr 26, 2017 at 3:28 AM Vlad Cojocaru <
>> vlad.cojocaru_at_mpi-muenster.mpg.de<mailto:vlad.cojocaru_at_mpi-
>> muenster.mpg.de>> wrote:
>> Dear all,
>>
>> Does anybody have experience in using PLUMED 2.3 with NAMD 2.12 ? On the
>> PLUMED website I only found patches for NAMD 2.8 and 2.9 and this is
>> quite old ... They also mention that many MD engines are PLUMED-enabled
>> by default and no extra compilation is needed ... Is NAMD 2.12
>> PLUMED-enabled ?
>>
>> Thanks for any thoughts on this
>>
>> Best wishes
>> Vlad
>>
>> --
>> Vlad Cojocaru, Ph.D., Project Group Leader
>> Department of Cell and Developmental Biology
>> Max Planck Institute for Molecular Biomedicine
>> R?ntgenstrasse 20, 48149 M?nster, Germany
>> Tel: +49-251-70365-324; Fax: +49-251-70365-399
>> Email: vlad.cojocaru[at]mpi-muenster.mpg.de<https://na01.safelinks.
>> protection.outlook.com/?url=https%3A%2F%2Furldefense.proofpo
>> int.com%2Fv2%2Furl%3Fu%3Dhttp-3A__mpi-2Dmuenster.mpg.de%26d%
>> 3DDwMDaQ%26c%3D8hUWFZcy2Z-Za5rBPlktOQ%26r%3D6cQ04kjNHUuxT8SD
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>> 9YyT3sI%26e%3D&data=02%7C01%7CJoshua.Vermaas%40nrel.gov%7Cac
>> 9535701b75407b48d108d48cc1c3cd%7Ca0f29d7e28cd4f5484427885aee
>> 7c080%7C1%7C0%7C636288211232382811&sdata=vYucXC2u8ce5OfD5%2B
>> WoW0oEhD4e0iki1MKFSoyQOHWw%3D&reserved=0>
>> http://www.mpi-muenster.mpg.de/43241/cojocaru
>> afelinks.protection.outlook.com/?url=https%3A%2F%2Furldefens
>> e.proofpoint.com%2Fv2%2Furl%3Fu%3Dhttp-3A__www.mpi-2Dmuenste
>> r.mpg.de_43241_cojocaru%26d%3DDwMDaQ%26c%3D8hUWFZcy2Z-Za5rBP
>> lktOQ%26r%3D6cQ04kjNHUuxT8SDe1wb0TtPDsnWRp4T4iwoYRLFpsY%26m%
>> 3D_Zz9bUqkIEGH7RTOlipIaePNEH15xgReQJEuzedxM7c%26s%3DvDnY094A
>> 499Un-8cH-90Yzvb6AfIL4NN23CRhKDBZG0%26e%3D&data=02%7C01%7CJo
>> shua.Vermaas%40nrel.gov%7Cac9535701b75407b48d108d48cc1c3cd%
>> 7Ca0f29d7e28cd4f5484427885aee7c080%7C1%7C0%7C636288211232392
>> 812&sdata=EKlgqp5T6KScw%2F8%2F1cA4dfRhp0EzAGxtiyMriDu3DkQ%3D&reserved=0>
>>
>>
>>
>> --
>> Vlad Cojocaru, Ph.D., Project Group Leader
>> Department of Cell and Developmental Biology
>> Max Planck Institute for Molecular Biomedicine
>> R?ntgenstrasse 20, 48149 M?nster, 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
>> afelinks.protection.outlook.com/?url=https%3A%2F%2Furldefens
>> e.proofpoint.com%2Fv2%2Furl%3Fu%3Dhttp-3A__www.mpi-2Dmuenste
>> r.mpg.de_43241_cojocaru%26d%3DDwMDaQ%26c%3D8hUWFZcy2Z-Za5rBP
>> lktOQ%26r%3D6cQ04kjNHUuxT8SDe1wb0TtPDsnWRp4T4iwoYRLFpsY%26m%
>> 3D_Zz9bUqkIEGH7RTOlipIaePNEH15xgReQJEuzedxM7c%26s%3DvDnY094A
>> 499Un-8cH-90Yzvb6AfIL4NN23CRhKDBZG0%26e%3D&data=02%7C01%7CJo
>> shua.Vermaas%40nrel.gov%7Cac9535701b75407b48d108d48cc1c3cd%
>> 7Ca0f29d7e28cd4f5484427885aee7c080%7C1%7C0%7C636288211232392
>> 812&sdata=EKlgqp5T6KScw%2F8%2F1cA4dfRhp0EzAGxtiyMriDu3DkQ%3D&reserved=0>
>>
>>
>>
>>
>
>
> --
> 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
>
>
> --
> Vlad Cojocaru, Ph.D., Project Group Leader
> Department of Cell and Developmental Biology
> Max Planck Institute for Molecular Biomedicine
> R√∂ntgenstrasse 20, 48149 M√ľnster, Germany
> Tel: +49-251-70365-324 <+49%20251%2070365324>; Fax: +49-251-70365-399 <+49%20251%2070365399>
> Email: vlad.cojocaru[at]mpi-muenster.mpg.dehttp://www.mpi-muenster.mpg.de/43241/cojocaru
>
>

-- 
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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