[gmx-users] system is exploding

[Justin A. Lemkul]

Quoting Baofu Qiao <qiaobf at gmail.com>:

>
> If you are really sure about the topology, the problem is the initial
> structure. Try to use PackMol to build it.
>

For simple molecules in water, there is no need for a complicated program like
packmol.  Such a configuration can easily be built in Gromacs.

I have yet to see any evidence of an error.  From the original post, it seems
that EM failed to start at all.

-Justin

> On 11/26/2010 11:42 AM, Olga Ivchenko wrote:
> > I tried today to run minimization in vacuum for my small molecules. This
> has
> > the same error.
> >
> > 2010/11/26 Baofu Qiao <qiaobf at gmail.com>
> >
> >
> >> Have you run the energy minimization (or further simulation to optimize
> >> the structure and test the FF) on the small molecule before you added it
> >> into water?
> >>
> >> On 11/26/2010 11:26 AM, Olga Ivchenko wrote:
> >>
> >>> Dear gromacs users,
> >>>
> >>> I am trying to run simulations for small molecules in water. Topology
> >>>
> >> files
> >>
> >>> I created by my self for charm ff. When I am trying to start energy
> >>> minimization I got an error:
> >>>
> >>>
> >>>  Steepest Descents:
> >>>
> >>> Tolerance (Fmax) = 1.00000e+00
> >>>
> >>> Number of steps = 1000
> >>>
> >>>
> >>> That's means my system is exploding. Please can you advice me on this,
> >>>
> >> what
> >>
> >>> I need to check.
> >>>
> >>> best,
> >>>
> >>> Olga
> >>>
> >>>
> >>>
> >>
> >> --
> >> ************************************
> >>  Dr. Baofu Qiao
> >>  Institute for Computational Physics
> >>  Universität Stuttgart
> >>  Pfaffenwaldring 27
> >>  70569 Stuttgart
> >>
> >>  Tel: +49(0)711 68563607
> >>  Fax: +49(0)711 68563658
> >>
> >> --
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> >>
> >
>
>
> --
> ************************************
>  Dr. Baofu Qiao
>  Institute for Computational Physics
>  Universität Stuttgart
>  Pfaffenwaldring 27
>  70569 Stuttgart
>
>  Tel: +49(0)711 68563607
>  Fax: +49(0)711 68563658
>
> --
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========================================

Justin A. Lemkul
Ph.D. Candidate
ICTAS Doctoral Scholar
MILES-IGERT Trainee
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu | (540) 231-9080
http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin

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