amber-developers: multiple targeted MD in amber11

From: David Mathews <>
Date: Thu, 03 Jul 2008 11:24:12 -0400

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 changes
to amber11 and, now that the amber tools are settling down for a release,
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 EM64
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 in
the manual and a test case. We call this multiply-targeted MD (mtmd).


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 - 06:07:32 PDT
Custom Search