[gmx-users] T-coupling different atoms in the same molecule?

David spoel at xray.bmc.uu.se
Sat Feb 21 21:21:02 CET 2004

On Sat, 2004-02-21 at 21:15, Michael Shirts wrote:
> So, is it possible to put different sets of atoms in the same molecule in
> different temperature coupling groups?  I can't really tell if this is
> possible or not from the documentation.
yes, just make custom groups
> Also, is it possible to put a distance restraint between two atoms on
> different molecules?
in principle yes, check the archives. for proteins you can merge the
chains (pdb2gmx -merge)
> Basically, I'm trying to link two molecules by a restraint -- I can either
> make it one molecule, and try to temperature couple the two parts seperately
> (I'm doing some non-physical things, so I'd like to temperture control both
> groups), OR I can link the two molecules together by a restraint.
> Thanks,
> Michael
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David van der Spoel, PhD, Assist. Prof., Molecular Biophysics group,
Dept. of Cell and Molecular Biology, Uppsala University.
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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