Re: namd 2.12 and plumed 2.3

From: Giacomo Fiorin (giacomo.fiorin_at_gmail.com)
Date: Wed Apr 26 2017 - 12:01:51 CDT

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.
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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
>
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-- 
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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