Hello,
Thank you very much for your answer. It has been of great help!
Almudena.
El 06/04/2011, a las 23:43, Jason Swails escribió:
> 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
>> _______________________________________________
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>> http://lists.ambermd.org/mailman/listinfo/amber
>>
>
>
>
> --
> Jason M. Swails
> Quantum Theory Project,
> University of Florida
> Ph.D. Candidate
> 352-392-4032
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Received on Thu Apr 07 2011 - 00:00:03 PDT
