[gmx-users] Re: requested for GROMACS package

Vitaly Chaban chaban at univer.kharkov.ua
Tue Aug 12 15:51:24 CEST 2008

> hello
> I am working with protien 1PGB having 56 amino acids (practical tutorial
> from GROMACS web site) for its simulation using the flexilbe water.
> the commands that i have run are :
> At later stsges of MD simulations ( i.e after position restrained MD), I
> have been getting few errors which are as follow:
> ---------------------------------------------------------------------------------------------------
> *./grompp –f run.mdp –p topol.top –c pr.gro –o run.tpr*
>  followed by
> *./mdrun –v –deffnm run*
> Range checking error:
> Explanation: During neighborsearching, we assign each particle to a grid
> based on its coordinates. If your system contains collisions or parameter
> errors that give particles very high velocities you might end up with some
> coordinates being +-Infinity or NaN (not-a-number). Obviously, we cannot
> put these on a grid, so this is usually where we detect those errors.
> Make sure your system is properly energy-minimized and that the potential
> energy seems reasonable before trying again.

You're just exploding. Try energy minimization (integrator=l_bfgs)
before running MD.

Obviously, you missed some stage of the example or it did not finish
correctly. You can also run the example from beginning carefully.

P.S. Justin is extremely strict today. :)

Vitaly V. Chaban
School of Chemistry
National University of Kharkiv
Svoboda sq., 4, Kharkiv 61077, Ukraine
email: chaban at univer.kharkov.ua
skype: vvchaban

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