[gmx-users] position restrained MD run?

Samuel Flores samuel.flores at yale.edu
Mon Aug 8 04:14:12 CEST 2005

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.  

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!  

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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