[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.

> Dima
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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