[gmx-users] position restrained MD run?

[Samuel Flores]

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!

Thanks

Sam