From: andrea spitaleri (spitaleri.andrea_at_hsr.it)
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:
http://www.plumed-code.org/made-with-plumed
>>
>> --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:
http://people.sissa.it/~laio/Publications/abstracts/48.php
hope it helps
and
>>
>> 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 Italy Tel: 0039-0226434348 Fax: 0039-0226434153 http://sites.google.com/site/andreaspitaleri/ http://biomolnmr.org/ http://www.linkedin.com/in/andreaspitaleri -------------------------------------------------------------
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