Re: vmd-l: About PLUMED with NAMD VMD

From: andrea spitaleri (
Date: Thu Feb 28 2013 - 02:46:34 CST

Hi there,

>> ---Can PLUMED be run with namd 2.9? What about CUDA version?

Yes, PLUMED can be used with namd. I think that the only GPU version available is the acemd software.

>> --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 may check here:

>> --Is any advantage provided by PLUMED with respect to the methods
>> implemented in NAMD?

It depends what kind of advantage you are looking for.

>> --Is PLUMED capable to deal with free energy?

PLUMED calculates free energy surface in the collective variable space. In PLUMED you can use
metadynamics approach to explore rare events and overcome large energetic barriers between minima.
Have look to:

hope it helps


>> Thanks
>> francesco pietra

Andrea Spitaleri PhD
Dulbecco Telethon Institute c/o Fondazione Centro San Raffaele
Centro di Genomica Traslazione e Bioinformatica
Biomolecular NMR Laboratory Dibit2 Basilica 3A2
Via Olgettina 58
20132 Milano
Tel: 0039-0226434348
Fax: 0039-0226434153

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