From: Giacomo Fiorin (giacomo.fiorin_at_gmail.com)
Date: Wed Feb 27 2013 - 02:39:27 CST
Hello, Francesco.
---Can PLUMED be run with namd 2.9? What about CUDA version?
>
Yes, I believe the patch should be compatible with CUDA.
> --Many publications using PLUMED are available in PLUMED web, dealing
> with various aspects, such as protein-protein interaction or
> conformational search, carried out with PLUMED implemented into
> various software. Is any collections of publications available by
> merely using colvars implemented in NAMD?
>
You could find e.g. the papers that cite the following article:
http://pubs.acs.org/doi/abs/10.1021/ct9004432
Although the article covers the most recent implementation of ABF, that
implementation is the one provided by colvars, and metadynamics is used in
the paper as well.
> --Is any advantage provided by PLUMED with respect to the methods
implemented in NAMD?
>
Aside from ABF, steered MD and umbrella sampling, colvars implements the
original version of metadynamics and the multiple-walkers variant
(parallelism without replica-exchange), both of which provide you a single
PMF to analyze.
By design, PLUMED covers those two but also the more variants of
metadynamics: those are bias-exchange metadynamics, temperature-exchange
metadynamics, reconnaissance metadynamics... To find the advantages of
each of the newer variants, you should refer to its paper, and to the
literature in general.
> --Is PLUMED capable to deal with free energy?
>
Yes, if you mean configurational free energy (i.e. not alchemical
difference).
> Thanks
>
> francesco pietra
>
>
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