[gmx-users] localized molecular dynamics

David van der Spoel spoel at xray.bmc.uu.se
Wed Dec 13 14:48:17 CET 2006

Giacomo Bastianelli wrote:
> Dear users,
> I was wondering if it is possible with gromacs
> to run a MD of a protein just in few residues (let's say a pocket).
> Does it reduce the calculation time for the dynamics?
> thanks in advance,
> Giacomo Bastianelli
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yes, you can combine freezing and energy_group exclusions for this 
purpose. you still have to compute the interaction between the mobile 
residues and the environment though.

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://folding.bmc.uu.se

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