[gmx-users] Longer scale simulations

David van der Spoel spoel at xray.bmc.uu.se
Tue Dec 9 15:41:01 CET 2003

On Tue, 2003-12-09 at 15:00, Ran Friedman wrote:
> Dear GMX users and developers,
> I'd like to simulate protein motions which will normally take longer than the scale of MD simulations.
> Are such calculations feasible using the SD or BD algorithms in Gromacs?
> Are you aware of any references to such calculations made using Gromacs?
> Regarding SD - is it possible to divide the system to a region were full MD takes place and a region where SD is effective?

we can not combine these. how long would you like to simulate? 50 - 100
ns is not a real problem ig you have a few dedicated linux boxes.

> Thank you,
> Ran.
> -- 
> ------------------------------------------------------
> Ran Friedman
> Laser laboratory for fast reactions in biology
> Department of biochemistry
> Faculty of life sciences
> Tel-Aviv university
> 972-3-6409824
> ------------------------------------------------------
David van der Spoel, PhD, Assist. 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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