spoel at xray.bmc.uu.se
Wed Jul 9 23:50:02 CEST 2003
On Wed, 2003-07-09 at 23:37, Nagy, Peter I. wrote:
> Dear Gromacs Users!
> I think, this problem has emerged many times, so please direct me
> if there are answers somewhere.
> I performed a 10 ps test run for a protein consisting of 26
> residues and about 600 water molecules. Everything went seemingly
> properly. When I looked at the protein dynamics using ngmx I found
> that the protein was much out of the box. I assume that a
> translational motion was allowed although the center of mass should
> not move, and originally the software places the protein within the
> box, I presume. There must be periodic boundary conditions, so the
> protein would remain solvated even leaving the box, yet I am worried
> about the translation.
> The question is: how could I keep the solute strictly within the
> box, thus
> preventing translation?
you can define center of mass motion removal group (com_groups IIRC)
but do you really want to stop the protein from diffusing?
You won't be able to calculate the diffusion constant!
> Thanks, Peter Nagy
Dr. David van der Spoel, Dept. of Cell and Molecular Biology
Husargatan 3, Box 596, 75124 Uppsala, Sweden
phone: 46 18 471 4205 fax: 46 18 511 755
spoel at xray.bmc.uu.se spoel at gromacs.org http://xray.bmc.uu.se/~spoel
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