[gmx-users] position restrained MD run?
spoel at xray.bmc.uu.se
Mon Aug 8 08:28:14 CEST 2005
On Sun, 2005-08-07 at 22:14 -0400, Samuel Flores wrote:
> Howdy all,
> I wonder if someone can help me do a position restrained MD run. I have
> read that when using a water box it is advisable to remove close contacts in
> this way. However when I do the analysis, I find protein atoms being thrown
> unnaturally large distances. This would not happen if the position
> restraints were working! The protein should be frozen, and only the water
> would move.
You sure that these are not PBC effects?
> When I go to look at the cpeptide demo script, I find that a position
> restrained run is being done. However when I view the cpeptide_pr
> trajectory in ngmx, I see that the protein is not restrained at all, but
> rather is wiggling happily in the water!
Restrained != frozen.
Restraints mean that the atoms can move about the restrained positions.
The average position should be very close to the restrained positions.
> What is going on? Is it possible to do a position restrained run? If
> someone could tell me why it's not happening in the cpeptide demo, I could
> make it work in my script. I've had colleagues come look at the problem,
> banged my head against the wall, and gotten nowhere.
> Any help is much appreciated!
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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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