[gmx-users] Fwd: Drug - Enzyme Tutorial

[Tsjerk Wassenaar]

Hi Fulya,

Did grompp give you any warnings? At what time did the error occur? At
the start of the simulation or later? Could you check the log file for
LINCS warnings, and try to track down the first occurrence? This would
help to be able to say some more than "your system is exploding".

Best,

Tsjerk

On 3/27/07, fulya caglar <fulyacaglar at yahoo.com> wrote:
>
>
> Note: forwarded message attached.
>
>  ________________________________
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> ---------- Forwarded message ----------
> From: fulya caglar <fulyacaglar at yahoo.com>
> To: gmx-users-request at gromacs.org
> Date: Mon, 26 Mar 2007 12:44:18 -0700 (PDT)
> Subject: Drug - Enzyme Tutorial
> Although I could run sucessfully speptide tutorial,while attempting the
> drug-enzyme tutorial  I am getting the following error message after the
> first mdrun command ( mdrun -s trp_em.tpr -o trp_em.trr -c trp_b4pr.pdb -g
> em.log –e em.edr);
> -----------------------------------------
> Warning: 1-4 interaction between 2100 and 2105 at distance 15.231 which is
> larger than the 1-4 table size 1.000 nm
> These are ignored for the rest of the simulation
> This usually means your system is exploding,
> if not, you should increase table-extension in your mdp file
> -------------------------------------------------------
> Program mdrun_mpi, 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 .. 19488 ]
> Please report this to the mailing list (gmx-users at gromacs.org)
>
> ---------------------------------------------------------------------------
>
>    I would be very glad to know why I get this type of error.  Thanks very
> much.
>
>    With thanks
>  Sincerely Fulya
>
>
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-- 
Tsjerk A. Wassenaar, Ph.D.
Junior UD (post-doc)
Biomolecular NMR, Bijvoet Center
Utrecht University
Padualaan 8
3584 CH Utrecht
The Netherlands
P: +31-30-2539931
F: +31-30-2537623