[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
> gmx-users mailing list gmx-users at gromacs.org
> Please don't post (un)subscribe requests to the list. Use the www
> interface or send it to gmx-users-request at gromacs.org.
> Can't post? Read http://www.gromacs.org/mailing_lists/users.php
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
More information about the gromacs.org_gmx-users