[gmx-users] localized molecular dynamics

[David van der Spoel]

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
> http://www.gromacs.org/mailman/listinfo/gmx-users
> 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.
________________________________________________________________________
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
++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++