[gmx-users] com motion
David van der Spoel
spoel at xray.bmc.uu.se
Fri Apr 4 11:56:02 CEST 2003
On Fri, 2003-04-04 at 11:14, Mustafa Toprakçý wrote:
> Dear Gromacs Team,
> I would like to ask one issue. I have defined a substrate-enzyme
> complex system, using pdb2gmx as 1 molecule in the .top file. I might
> have also defined the same system as 2 molecules such as protein and
> ligand in the .top file.
> I am simülating center of mass motion, Does it differ for the program
> to see the system as one or two molecules in the aspect of ligand center
> of mass simülation?
All groups must be mutually exclusive, that is for COM an atom can only
be in one group, same for energies. However, energy groups and COM
groups must not be the same, they can, but it's not necessary.
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Dr. David van der Spoel, Dept. of Cell & Mol. 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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