[gmx-users] alter the box
David van der Spoel
spoel at xray.bmc.uu.se
Wed Jul 7 14:21:46 CEST 2004
On Wed, 2004-07-07 at 14:14, Dmitry Kovalsky wrote:
> Hi there
> I'm simulating my protein with lots of water molecules and ions included. My
> box type is octahedron. Now I want to decrease the box dimensions in order
> to spped up my calculations. Is there a way I can do this after which the
> velocities of the remaining atoms will be preserved and I can readily
> continue the simulation? Or I should extract protein, recreate a new box,
> fill it with waters and so on?
Easiest is probably to remove random water molecules and then
equilibrate with pressure coupling.
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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