[gmx-users] Variable ci problem!

Esther ecaballe at uoregon.edu
Thu Aug 3 01:09:03 CEST 2006

Samuel Silva Pita wrote:
> Dear GMXers,
> I had built my molecular topology "by hand" an when I was minimisate the energy of my system gromacs 3.3.1 give this error message:
> "Steepest Descents:
>    Tolerance (Fmax)   =  1.00000e+01
>    Number of steps    =        10000
> Step=    0, Dmax= 1.0e-02 nm, Epot= -6.12087e+04 Fmax= 1.82761e+04, atom= 6018
Atom 6018 might be the problem. Could it be a bad contact? Look at the 
.gro file to see who 6018 is, and then use some visualization software 
(ie, Pymol) to look at it...
Also could be that your topology had some issues...
> -------------------------------------------------------
> Program mdrun_331, VERSION 3.3.1
> Source code file: nsgrid.c, line: 226
> 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.
> Variable ci has value -2147483648. It should have been within [ 0 .. 384 ]
> Please report this to the mailing list (gmx-users at gromacs.org)
> -------------------------------------------------------"
>  I saw at ancient mailing lists  and I am not using more than one processors -like the persons who asked before about this theme!- and I wonder if it is a bug of grompp-331, is not? 
Probably is due to the starting structure or the topology.
>  Another important point is I had tried to include in genbox the option -ci "my molecule".gro and -cp "box_data_from_editconf".gro and the error remains.
>  The problem persists and I not know how I can solve this. Can anyone helps me about this problem? 
> Sincerely,
> Samuel Pita.
> "Do not wear yourself out to get rich;do not trust your own cleverness.  Cast but a glance at riches, and they are gone, for they will surely sprout wings and fly off to the sky like an eagle."(Proverbs23:4-5)
> ============================================
> _______________________________________________
> 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.
> Can't post? Read http://www.gromacs.org/mailing_lists/users.php

Esther Caballero-Manrique
Graduate Teaching Fellow
Chemistry Department
1253 University of Oregon
Eugene, OR 97403 (USA)

More information about the gromacs.org_gmx-users mailing list