Re: amber-developers: multiple targeted MD in amber11

From: Volodymyr Babin <>
Date: Thu, 3 Jul 2008 12:32:26 -0400 (EDT)

Dear Prof. David Mathews,

thank you. I believe that the ncsu_pmd subsystem already implements
this functionality (as a particular case when all collective variables
are of MULTI_RMSD type with just one "group" each). In addition, the
ncsu_pmd also modifies REMD exchange probabilities so that it should
be possible to do umbrella sampling using parallel tempering.

With kind regards,

On Thu, July 3, 2008 11:24, David Mathews wrote:
> Hi All,
> Matt Seetin, from my group, has added a new feature to amber11 that
> allows
> for targeted MD to multiple targets (with multiple force constants,
etc). We are using this for umbrella sampling. I've committed the
> to amber11 and, now that the amber tools are settling down for a
> we would appreciate any feedback. Of course, we want to know if we have
broken anything (we are restricted to testing with various flavors of
> linux using ifort, g95, and gfortran), but we also want to know whether
this has enough broad appeal to keep in amber11. There is a new entry
> the manual and a test case. We call this multiply-targeted MD (mtmd).
> Thanks,
> Dave
> ___________________________________________________
> David Mathews, MD, PhD
> Assistant Professor of Biochemistry & Biophysics
> and of Biostatistics & Computational Biology
> University of Rochester Medical Center
> Room 3-6830
> 601 Elmwood Avenue, Box 712
> Rochester, New York 14642
Received on Sun Jul 06 2008 - 06:07:33 PDT
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