[gmx-users] Mdrun problems

[David van der Spoel]

On Thu, 2005-06-02 at 13:20 +0100, Farid Sa'Adedin wrote:
> Topology and input structure are fine.
> 
> Any other ideas?

PBC.

check which energy becomes nan.


> 
> Farid
> 
> 
> Quoting Anton Feenstra <feenstra at few.vu.nl>:
> 
> > Farid Sa'Adedin wrote:
> >
> > > Dear GROMACS users,
> > >
> > > I have encountered a problem when I try to energy minimise a bilayer that I
> > > created.  When I ran it on grompp no errors were detected.  But when I did
> > > mdrun -v
> > >
> > > The simulation starts to run but then after a few steps it brings this
> > error
> > > message:
> > >
> > > Stepwise too small (6.10352e-07nm) Converged to the machine precision, but
> > not
> > > to the requested position (1000)
> > >
> > > Steepest descent did not converge in 15 steps
> > >
> > > Potential Energy = nan
> > > Maximum Force 1.28603e+7
> > >
> > > I have tried changing various options on the mdp file but to no avail.
> > >
> > > If anyone knows what I can do to rectify the situation it would be most
> > > appreciated.
> >
> > Check your input structure, there are defenitely things wrong there, or
> > it could be your topology.
> >
> >
> > --
> > Groetjes,
> >
> > Anton
> >
> > * NOTE: New Phone & Fax numbers (below) *
> >
> >   _____________ _______________________________________________________
> > |             |                                                       |
> > |  _   _  ___,| K. Anton Feenstra                                     |
> > | / \ / \'| | | Dept. of Pharmacochem. - Vrije Universiteit Amsterdam |
> > |(   |   )| | | De Boelelaan 1083 - 1081 HV Amsterdam - Netherlands   |
> > | \_/ \_/ | | | Tel: +31 20 59 87608 - Fax: +31 20 59 87610           |
> > |             | Feenstra at few.vu.nl - www.few.vu.nl/~feenstra/         |
> > |             | "If You See Me Getting High, Knock Me Down" (RHCP)    |
> > |_____________|_______________________________________________________|
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> 
> 
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-- 
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://xray.bmc.uu.se/~spoel
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