[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?
> Regards.
> Pedro.

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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