[gmx-users] Longer scale simulations

[Ran Friedman]

If it was possible, I'd like to simulate my system for around 100ns. However, this is too complex for me now, as I just want to test a hypothesis.

Ran.

David van der Spoel wrote:

> 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.
> ________________________________________________________________________
> 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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--
------------------------------------------------------
Ran Friedman
Laser laboratory for fast reactions in biology
Department of biochemistry
Faculty of life sciences
Tel-Aviv university
972-3-6409824
------------------------------------------------------


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