[gmx-users] (no subject)
spoel at xray.bmc.uu.se
Mon Jul 15 20:51:39 CEST 2002
On Mon, 2002-07-15 at 20:26, J Lorieau wrote:
> 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.
This is not a problem, but if you really don't want it to happen you can
apply center-of-mass motion removal to your protein and solvent
separately if you wish by specifying com-groups.
> 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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Dr. David van der Spoel, Biomedical center, Dept. of Biochemistry
Husargatan 3, Box 576, 75123 Uppsala, Sweden
phone: 46 18 471 4205 fax: 46 18 511 755
spoel at xray.bmc.uu.se spoel at gromacs.org http://zorn.bmc.uu.se/~spoel
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