[gmx-users] Problems in C8 and C9 chains equilibration
tsjerkw at gmail.com
Tue Mar 13 21:44:50 CET 2007
Did you first try the readily available C6? I would not suspect any
problem with C8/9/... To me, the fact that you run into segfaults
suggests that you got the topology wrong, or you're doing something
wrong with setting up the system. I assume you did perform energy
minimization and position restraint MD. You should be able to take the
same strategy for C8/9/... as you would for C6 (for which you know
that the topology is correct).
Don't try to fight symptoms, try to find the source.
On 3/13/07, Jones de Andrade <johannesrs at gmail.com> wrote:
> 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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Tsjerk A. Wassenaar, Ph.D.
Junior UD (post-doc)
Biomolecular NMR, Bijvoet Center
3584 CH Utrecht
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