[gmx-users] Center of Simulation Box

[David]

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).

>  Thanks,
>  Indira 
> 
> 
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-- 
Groeten, David.
________________________________________________________________________
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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