[gmx-users] MD on part of protein

David spoel at xray.bmc.uu.se
Wed Apr 6 06:34:08 CEST 2005

On Tue, 2005-04-05 at 16:14 -0400, deepa rajamani wrote:
> Hi,
> Is it possible to run MD on a small part of a large protein by defining a
> small box region, while using the periodic boundary conditions.
> When I try to make a small box by defining the atoms in an index file, the
> program complains of difference in number of coordinates between the .gro
> file and .top file when generating the .tpr  file. Any suggestions?
freeze part of your system, with or without energy exclusions. check
online manual.

> Deepa
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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
spoel at xray.bmc.uu.se    spoel at gromacs.org   http://xray.bmc.uu.se/~spoel

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