[gmx-users] Re: help

Justin A. Lemkul jalemkul at vt.edu
Fri Feb 1 16:39:41 CET 2008

Quoting mahendra awale <mahendra123awale at gmail.com>:

> hi
> dear sir
> i am mahendra awale doing M.S in NIPER INDIA in pharmacoinformatics
> i am running MD simulation
> i have a problem while running MD would u please help me

It is best to keep Gromacs-related questions on the users' list, and I am
copying the other members so that an archived copy of this message will be
preserved for others to use.  Please send questions to the gmx-users list in
the future.  You also have a much better chance of reaching someone who knows
how to solve your problem.  See below for my ideas on your situation.

> 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.
> /Please follow the advice in the above two sentences.

It is hard to say what might be the problem, but it appears that mdrun has
already told you.  What step is this - minimization, equilibration, or
Did you minimize and/or equilibrate your system, and if yes, then how?  What is
in your system - a simple protein, or some sort of complex system?  Without this
information, you will likely get no useful help.

Check the gmx-users archive for similar problems.  This particular issue has
been discussed dozens of times in recent memory.  Also consult the wiki site
(wiki.gromacs.org), specifically:



If you need further help, it will be useful to send the message to the gmx-users
list, and include:
1. What your system contains
2. How you have minimized or equilibrated your system
3. The text of your .mdp file


> thank u
> looking forward for u r reply


Justin A. Lemkul
Graduate Research Assistant
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul at vt.edu | (540) 231-9080


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