Hello,
This functionality IS in amber11 (and I'm guessing amber10 as well, but I'm
not certain about that). It's accessed via -rem 2 with sander.LES.MPI.
However, this functionality is undocumented in the Amber11 manual as far as
I can tell. I couldn't find it described in either the LES or REMD sections
of the manual. This omission was done either because the functionality is
incomplete or because they didn't have time to properly document the feature
(perhaps those who know more about this code can answer more fully).
In any case, this is advanced functionality. You'll have to become
comfortable with setting up LES simulations and REMD simulations. There may
be special considerations involved with setting up LES/REMD simulations as
well that I don't know about.
In any case, the only "documentation" that exists is the code itself (unless
I missed where it was in the manual). For relevant source code files, see
sander.f, runmd.f, and remd.f in $AMBERHOME/src/sander.
Hope this helps,
Jason
On Tue, Apr 5, 2011 at 4:10 AM, Almudena Pino <almupino.gmail.com> wrote:
> Dear Amber users,
>
> I was checking the literature about LES when I have come across the paper
> entitled "Modified Replica Exchange Simulation Methods for Local Structure
> Refinement", published in J. Chem. Phys. B back in 2005. I find the content
> very interesting and I'd like to try the PREMD or LREMD described in it for
> refining some small loops of an homology model, but when I have checked
> Amber 9 tutorial for those modifications to be implemented in the REMD
> section, I have not been able to find anything about it.
>
> Are these modifications of the method available in the latest versions of
> Amber?
>
> Thank you very much.
>
> Almudena
> _______________________________________________
> AMBER mailing list
> AMBER.ambermd.org
> http://lists.ambermd.org/mailman/listinfo/amber
>
--
Jason M. Swails
Quantum Theory Project,
University of Florida
Ph.D. Candidate
352-392-4032
_______________________________________________
AMBER mailing list
AMBER.ambermd.org
http://lists.ambermd.org/mailman/listinfo/amber
Received on Wed Apr 06 2011 - 15:30:02 PDT
