[gmx-users] Re: Gromacs simulation of infinite systems
spoel at xray.bmc.uu.se
Tue Dec 3 18:32:01 CET 2002
On Tue, 2002-12-03 at 17:20, Ester Chiessi wrote:
> Hi David,
> I found your e-mail address from the Gromacs mailing list archive.
> I disturb you for a question about the possibility to simulate chemical
> bonds across boundaries in PBC with gromacs.
> I spent a lot of energy to try to perform a md calculation of an
> 'infinite' polymer chain, without promising results.
> The dynamics goes on if I don't apply any constraint to bonds ( both
> LINKS and SHAKE give errors) but the timestep must be very small (0.0002
> I red you simulated diamond. Please, could you describe me the
> conditions you used?
You have to set an environment variable
setenv GMXFULLPBC 1
It depends on your system, but you can always use shake for hydrogens I
think and still use a timestep of 1 fs. (At least as long as the
hydrogens and the heavy atom are in the same charge group).
I can make it an mdp option.
> Thanks a lot for your help.
> Ester Chiessi
> Dipartimento di Scienze e Tecnologie Chimiche
> Universita' di Roma "Tor Vergata"
> Via della Ricerca Scientifica
> 00133 Roma (Italy)
> e-mail: ester.chiessi at uniroma2.it
> Phone: 39*6*72594462
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://xray.bmc.uu.se/~spoel
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