[gmx-users] Mdrun problems

[Farid Sa'Adedin]

Topology and input structure are fine.

Any other ideas?

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)    |
> |_____________|_______________________________________________________|
> _______________________________________________
> gmx-users mailing list
> gmx-users at gromacs.org
> http://www.gromacs.org/mailman/listinfo/gmx-users
> Please don't post (un)subscribe requests to the list. Use the
> www interface or send it to gmx-users-request at gromacs.org.
>