From: Vlad Cojocaru (vlad.cojocaru_at_mpi-muenster.mpg.de)
Date: Tue May 02 2017 - 09:00:14 CDT
Dear Giacomo,
Thanks a lot for the explanation ... Unfortunately, I am not that good
with the NAMD code and I am afraid, I may mess things up if I try to
modify myself. I attach here the current Plumed 2.3.1 patch that I used
to compile NAMD 2.12 ... If you or somebody else on the list could
advise me on how to modify this patch to actually fix the behavior in
NPT simulations, I would be very grateful. Of course, if this is easy to
do and does not require a massive effort from anyone.
Cheers
Vlad
On 05/02/2017 03:38 PM, Giacomo Fiorin wrote:
> 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.mpg.de
> <mailto:vlad.cojocaru_at_mpi-muenster.mpg.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 <mailto: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><mailto: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 <tel:%2B49-251-70365-324>; Fax:
>> +49-251-70365-399 <tel:%2B49-251-70365-399>
>> Email: vlad.cojocaru[at]mpi-muenster.mpg.de
>> <http://mpi-muenster.mpg.de><https://na01.safelinks.protection.outlook.com/?url=https%3A%2F%2Furldefense.proofpoint.com%2Fv2%2Furl%3Fu%3Dhttp-3A__mpi-2Dmuenster.mpg.de%26d%3DDwMDaQ%26c%3D8hUWFZcy2Z-Za5rBPlktOQ%26r%3D6cQ04kjNHUuxT8SDe1wb0TtPDsnWRp4T4iwoYRLFpsY%26m%3D_Zz9bUqkIEGH7RTOlipIaePNEH15xgReQJEuzedxM7c%26s%3DoPMJw3-Q8K8kipSpMFF349CGxurjS2CMS0L19YyT3sI%26e%3D&data=02%7C01%7CJoshua.Vermaas%40nrel.gov%7Cac9535701b75407b48d108d48cc1c3cd%7Ca0f29d7e28cd4f5484427885aee7c080%7C1%7C0%7C636288211232382811&sdata=vYucXC2u8ce5OfD5%2BWoW0oEhD4e0iki1MKFSoyQOHWw%3D&reserved=0
>> <https://na01.safelinks.protection.outlook.com/?url=https%3A%2F%2Furldefense.proofpoint.com%2Fv2%2Furl%3Fu%3Dhttp-3A__mpi-2Dmuenster.mpg.de%26d%3DDwMDaQ%26c%3D8hUWFZcy2Z-Za5rBPlktOQ%26r%3D6cQ04kjNHUuxT8SDe1wb0TtPDsnWRp4T4iwoYRLFpsY%26m%3D_Zz9bUqkIEGH7RTOlipIaePNEH15xgReQJEuzedxM7c%26s%3DoPMJw3-Q8K8kipSpMFF349CGxurjS2CMS0L19YyT3sI%26e%3D&data=02%7C01%7CJoshua.Vermaas%40nrel.gov%7Cac9535701b75407b48d108d48cc1c3cd%7Ca0f29d7e28cd4f5484427885aee7c080%7C1%7C0%7C636288211232382811&sdata=vYucXC2u8ce5OfD5%2BWoW0oEhD4e0iki1MKFSoyQOHWw%3D&reserved=0>>
>> http://www.mpi-muenster.mpg.de/43241/cojocaru
>> <http://www.mpi-muenster.mpg.de/43241/cojocaru><https://na01.safelinks.protection.outlook.com/?url=https%3A%2F%2Furldefense.proofpoint.com%2Fv2%2Furl%3Fu%3Dhttp-3A__www.mpi-2Dmuenster.mpg.de_43241_cojocaru%26d%3DDwMDaQ%26c%3D8hUWFZcy2Z-Za5rBPlktOQ%26r%3D6cQ04kjNHUuxT8SDe1wb0TtPDsnWRp4T4iwoYRLFpsY%26m%3D_Zz9bUqkIEGH7RTOlipIaePNEH15xgReQJEuzedxM7c%26s%3DvDnY094A499Un-8cH-90Yzvb6AfIL4NN23CRhKDBZG0%26e%3D&data=02%7C01%7CJoshua.Vermaas%40nrel.gov%7Cac9535701b75407b48d108d48cc1c3cd%7Ca0f29d7e28cd4f5484427885aee7c080%7C1%7C0%7C636288211232392812&sdata=EKlgqp5T6KScw%2F8%2F1cA4dfRhp0EzAGxtiyMriDu3DkQ%3D&reserved=0
>> <https://na01.safelinks.protection.outlook.com/?url=https%3A%2F%2Furldefense.proofpoint.com%2Fv2%2Furl%3Fu%3Dhttp-3A__www.mpi-2Dmuenster.mpg.de_43241_cojocaru%26d%3DDwMDaQ%26c%3D8hUWFZcy2Z-Za5rBPlktOQ%26r%3D6cQ04kjNHUuxT8SDe1wb0TtPDsnWRp4T4iwoYRLFpsY%26m%3D_Zz9bUqkIEGH7RTOlipIaePNEH15xgReQJEuzedxM7c%26s%3DvDnY094A499Un-8cH-90Yzvb6AfIL4NN23CRhKDBZG0%26e%3D&data=02%7C01%7CJoshua.Vermaas%40nrel.gov%7Cac9535701b75407b48d108d48cc1c3cd%7Ca0f29d7e28cd4f5484427885aee7c080%7C1%7C0%7C636288211232392812&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 <tel:%2B49-251-70365-324>; Fax:
>> +49-251-70365-399 <tel:%2B49-251-70365-399>
>> Email: vlad.cojocaru[at]mpi-muenster.mpg.de
>> <http://mpi-muenster.mpg.de>
>> http://www.mpi-muenster.mpg.de/43241/cojocaru
>> <http://www.mpi-muenster.mpg.de/43241/cojocaru><https://na01.safelinks.protection.outlook.com/?url=https%3A%2F%2Furldefense.proofpoint.com%2Fv2%2Furl%3Fu%3Dhttp-3A__www.mpi-2Dmuenster.mpg.de_43241_cojocaru%26d%3DDwMDaQ%26c%3D8hUWFZcy2Z-Za5rBPlktOQ%26r%3D6cQ04kjNHUuxT8SDe1wb0TtPDsnWRp4T4iwoYRLFpsY%26m%3D_Zz9bUqkIEGH7RTOlipIaePNEH15xgReQJEuzedxM7c%26s%3DvDnY094A499Un-8cH-90Yzvb6AfIL4NN23CRhKDBZG0%26e%3D&data=02%7C01%7CJoshua.Vermaas%40nrel.gov%7Cac9535701b75407b48d108d48cc1c3cd%7Ca0f29d7e28cd4f5484427885aee7c080%7C1%7C0%7C636288211232392812&sdata=EKlgqp5T6KScw%2F8%2F1cA4dfRhp0EzAGxtiyMriDu3DkQ%3D&reserved=0
>> <https://na01.safelinks.protection.outlook.com/?url=https%3A%2F%2Furldefense.proofpoint.com%2Fv2%2Furl%3Fu%3Dhttp-3A__www.mpi-2Dmuenster.mpg.de_43241_cojocaru%26d%3DDwMDaQ%26c%3D8hUWFZcy2Z-Za5rBPlktOQ%26r%3D6cQ04kjNHUuxT8SDe1wb0TtPDsnWRp4T4iwoYRLFpsY%26m%3D_Zz9bUqkIEGH7RTOlipIaePNEH15xgReQJEuzedxM7c%26s%3DvDnY094A499Un-8cH-90Yzvb6AfIL4NN23CRhKDBZG0%26e%3D&data=02%7C01%7CJoshua.Vermaas%40nrel.gov%7Cac9535701b75407b48d108d48cc1c3cd%7Ca0f29d7e28cd4f5484427885aee7c080%7C1%7C0%7C636288211232392812&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 <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 <tel:+49%20251%2070365324>; Fax:
> +49-251-70365-399 <tel:+49%20251%2070365399>Email:
> vlad.cojocaru[at]mpi-muenster.mpg.de <http://mpi-muenster.mpg.de>
> http://www.mpi-muenster.mpg.de/43241/cojocaru
> <http://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
> <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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