[gmx-users] Mdrun Error

Venky venky.agas at gmail.com
Sat Jun 3 07:31:40 CEST 2006

Hi gmx-users,

I am setting up a membrane inserted protein simulation.
The protein is mutated at a specific place and attached to a label and
this is inserted into the POPC membrane (434 lipids). The label is a
small molecule whose force field params were generated on PRODRG
Everything was setup fine but when I try running the energy
minimisation I get the following error


Program mdrun, 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 .. 3179 ]
Please report this to the mailing list (gmx-users at gromacs.org)

What does it mean and how to go about correcting it? Thanks in advance.


Venky Krishnamani
Graduate Student,
Dr. Janos K. Lanyi Lab
Univerisity of California, Irvine
Irvine, CA
(949) 202-9466

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