Re: namd 2.12 and plumed 2.3

From: Vermaas, Joshua (Joshua.Vermaas_at_nrel.gov)
Date: Wed Apr 26 2017 - 11:43:41 CDT

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
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--
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/cojocaruuxT8SDe1wb0TtPDsnWRp4T4iwoYRLFpsY%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>

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