[gmx-users] Center of Simulation Box
spoel at xray.bmc.uu.se
Sat Sep 7 09:23:57 CEST 2002
On Fri, 2002-09-06 at 16:59, Shrivastava, Indira (NCI) wrote:
> Hi Gromacs_users,
> I have a simulation of a protein in a bilayer, in which,
> after the equlibration stage, (in which I fixed the protein and allowed
> the lipid and water molecules to move), the protein has shifted
> w.r.t to the center of the simulation box. That is, the center
> of the protein and the center of the simulation box do not coincide.
> Would it be alright to go ahead and do the production run or would
> it be incorrect?
This is not a problem. If you plan to do very long runs (many ns) you
may want to apply center of mass motion removal to separate groups (i.e.
SOLvent+Ions in one group and Lipids+Protein in another).
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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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