[gmx-users] Problems in C8 and C9 chains equilibration

Jones de Andrade johannesrs at gmail.com
Tue Mar 13 21:27:32 CET 2007

Hi all.

first, thanks a lot!  :)

Pedro: I've already expanded the box increadibly much (say, 200
angstrons in each direction), and the problem still remains. I mean,
expanded it from an original box with size to fit the experimental

Low temperatures where already tested in the C9 but not in the C8,
I'll try later. I've tried 98.15K for 200ps, but at the moment I don't
quite remember if it blowed at that temperature or when I tried to
increase it.

Will try again later and let you know.

David: I really haven't thought about this option. I'll try later, but
isn't it a dangerous behaviour such high pressure and low
equilibration time at same time?

Thank's a lot, any other clue will be also very thankfull. I'll test
those today or tomorrow and let you know. But really thanks in
advance.  :)

Sincerally yours,


On 3/13/07, David van der Spoel <spoel at xray.bmc.uu.se> wrote:
> 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
> pressure.
> --
> David.
> ________________________________________________________________________
> 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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