Mark Abraham wrote:
Huey Ling Tan wrote:
Dear all ,
thank you for those comments, we are aware of the paper. However, we
are not sure how to implement the replica exchange in gromacs. We
would like to run a set of replicas in which each replica corresponds
to a different set of umbrella parameters. However, when setting up a
replica exchange run, all .tpr files use the same .ppa file so that
each replica will have the same umbrella potential parameters. Do
you know how to get around this problem.
You will have to change the code to implement this algorithm.'
But first check the pull code in the cvs version of gromacs, where all
options have been moved to the mdp file.
Mark
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David.
________________________________________________________________________
David van der Spoel, PhD, Assoc. Prof., Molecular Biophysics group,
Dept. of Cell and Molecular Biology, Uppsala University.
Husargatan 3, Box 596, 75124 Uppsala, Sweden
phone: 46 18 471 4205 fax: 46 18 511 755
[EMAIL PROTECTED] [EMAIL PROTECTED] http://folding.bmc.uu.se
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