AMBER Archive (2002)

Subject: Re: SHAKE troubles

From: Stéphane Teletchéa (steletch_at_biomedicale.univ-paris5.fr)
Date: Fri May 31 2002 - 04:45:48 CDT

I think it is may be linked to the size of the box. The problem certainly
occurs because you didn't respect the 'law' which states that to have an
efficient PME simulation, one needs a cutoff smaller than the distance
between the solute and the faces of the box : for example 10 Angstroems for a
9 Angstroems cutoff.
If it works with smaller values, i think the reason is coming from that point.
Stef

Le Vendredi 31 Mai 2002 10:50, Arvid Soederhaell a écrit :
> Thanks for the interest in my SHAKE problems!
>
> Well, I have still not succeded to get my membrane-water simulation
> running, but it seems as if i'm not the only one who have had this
> problem, as indicated in the FAQ list (BLOWUP and SHAKE).
>
> Let me explain the situation in more detail...
> The simulaiton contains lipids, which have strongly charged headgroups.
> (Phosphor has a charge of about +1, surrounded by 4 oxygens wiht a charge
> of about -0.7 each.) The SHAKE problems occur when the cutoff (CUT) is
> increased from 8-9 angstroms to 11-12 angstroms. Before the increase the
> system is prefectly stable (several nanoseconds) using NVT and NPT
> anisotropic thermo/baro-stats. After the increase of cutoff the system
> becomes quite unstable, but it does not blow up immediately. Sometimes it
> runs for 40-50 ps and then crash. This happens in both NVT and NPT
> ensembles. The temperature is set to 323 Kelvin, which suggests that a
> shorter timestep should be used, but no... 1 fs timestep does not work,
> even 0.5 fs makes the system blow up.
>
> I have tryed to run minimizations using a long cutoff before restarting
> the dynamics, but this does not improve the situation.
>
> I believe that it has something to do wiht the strong charges of the lipid
> head groups, but i don't understand what....
>
> On Wed, 29 May 2002, David Case wrote:
> > On Wed, May 29, 2002, Arvid Soederhaell wrote:
> > > I have some problems with SHAKE that I do not understand. I get the
> > > error message
> > >
> > > COORDINATE RESETTING CANNOT BE ACCOMPLISHED,
> > > DEVIATION IS TOO LARGE
> > > NITER, NIT, LL, I AND J ARE : 0 0 1963 3195 3196
> >
> > If the problem happens at the beginning of a run, there is probably
> > something wrong with the energies or coordinates. Try minimization
> > without SHAKE for a few hundred steps.
> >
> > If the problem occurs in the "middle" of an otherwise stable simulation,
> > be sure that vlimit is set (to, say 20 or so). This is the default in
> > Amber 7, but I think it is not set by default in earlier versions.
> >
> > ....good luck...dac
> >
> > --
> >
> > ==================================================================
> > David A. Case | e-mail: case_at_scripps.edu
> > Dept. of Molecular Biology, TPC15 | fax: +1-858-784-8896
> > The Scripps Research Institute | phone: +1-858-784-9768
> > 10550 N. Torrey Pines Rd. | home page:
> > La Jolla CA 92037 USA | http://www.scripps.edu/case
> > ==================================================================