From: Giacomo Fiorin (giacomo.fiorin_at_gmail.com)
Date: Wed Feb 27 2013 - 02:39:27 CST
---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:
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
> francesco pietra
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