[gmx-users] (no subject)

J Lorieau jll2006 at columbia.edu
Mon Jul 15 20:26:37 CEST 2002


	I have a simple question, unfortunately. I'm simulating 1A30 - HIV
protease in box of water. HIV PR is a dimer. After about 1 ns of
simulation, the protein COM drift out of the box.

	I've tried applying the comm_mode = Linear and nstcomm to every step.
This hasn't helped my situation. Do I need to run it in position
restraint mode. Also, by default was does position restraint restrain?
Should I be applying it for my standard MD runs, in monitoring
conformational dynamics - I quite sure I'm not suppose to, but I thought
I'd ask.

	I'm running my simulation on 2 nodes. However, I don't think that
affects anything.

I appreciate the help, Thanks

Justin Lorieau 

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