[gmx-users] position restrained MD run?

David 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!
> Thanks
> Sam 
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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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