From: davide branduardi (davide.branduardi_at_gmail.com)
Date: Wed Feb 27 2013 - 02:41:14 CST
Hi Francesco,
I just can reply for what I know from the PLUMED side.
1) The public version of PLUMED does not contain the patch for namd2.9
I have a private one which is under testing. If you want to give a
try contact me privately.
In the next future a new release of PLUMED will be out and there
we hope to include namd2.9 as well.
Concerning the CUDA version I don't know if it's compatible. Never
tried myself. I suspect that it is but
depending on what you're doing with PLUMED, you can have some
overhead which might
serialize your code and kill efficiency. For simple variables
there is minimal overhead.
2) Plumed deals with free energy methods. You can have a look to the
manual at http://www.plumed-code.org/
or https://sites.google.com/site/plumedtutorial2010/
3) Concerning its advantage over NAMD implementation my opinion is
that you have to dig into both their manuals to see which
one contains the features that you're looking for to succeed in
your project. But probably Giacomo can comment more on this.
Hope that helps.
Davide
On Wed, Feb 27, 2013 at 9:16 AM, Francesco Pietra <chiendarret_at_gmail.com> wrote:
> Hello:
> I came across unanswered questions that I summarize here. I assume to
> have missed answers.
>
> As a PLUMED plugin is now available with VMD:
>
> ---Can PLUMED be run with namd 2.9? What about CUDA version?
>
> --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?
>
> --Is any advantage provided by PLUMED with respect to the methods
> implemented in NAMD?
>
> --Is PLUMED capable to deal with free energy?
>
> Thanks
>
> francesco pietra
>
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