[gmx-users] Problems in C8 and C9 chains equilibration
David van der Spoel
spoel at xray.bmc.uu.se
Tue Mar 13 20:32:46 CET 2007
Pedro Alexandre de Araújo Gomes Lapido Loureiro wrote:
> Hi Jones,
> Another option is to begin the simulation at very low temperatures and
> increasing it at, say, every 500 ps.
> But it seems that your starting configuration has some problem, maybe
> too high a density?
> Comparing with the experimental value, how is your density?
Another related strategy is to first simulate a single molecule in a box
of say 2 x 2 x 2 nm, then use genconf to multiply the conformation to
the desired number (this way there is no overlap) and then simulate at
high pressure to shrink the box again. Finally equilibrate at normal
David van der Spoel, PhD, Assoc. 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://folding.bmc.uu.se
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