From: Vlad Cojocaru (vlad.cojocaru_at_mpi-muenster.mpg.de)
Date: Tue May 02 2017 - 10:33:34 CDT
Compilation went fine with the patch from github. Thanks again,
Giacomo! ... We will start testing and see if we spot any issues ..
Thanks to Josh for sharing the NAMD 2.11 patches
Vlad
On 05/02/2017 05:17 PM, Vlad Cojocaru wrote:
> :-);-) .. thanks a lot ... I assume I can simply take the patches you
> modified and apply them with the plumed 2.3 I already compiled .. Or,
> is there any need to recompile this specific plumed tree ? I will try
> it later tonight and let you know
>
> Vlad
>
> P.S: Maybe we will manage to get funding for a second edition of the
> Workshop :-) ... Indeed, it was fun ....
>
>
> On 05/02/2017 04:45 PM, Giacomo Fiorin wrote:
>> OK, OK, I guess I owe you one from the very nice workshop in Münster...
>>
>> Try this copy and let me know:
>> https://github.com/giacomofiorin/plumed2/tree/namd-updates
>>
>> On Tue, May 2, 2017 at 10:00 AM, Vlad Cojocaru
>> <vlad.cojocaru_at_mpi-muenster.mpg.de
>> <mailto:vlad.cojocaru_at_mpi-muenster.mpg.de>> wrote:
>>
>> 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 <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
> --
> 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
-- 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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