[gmx-users] mdrun problem

leafyoung81-group at yahoo.com leafyoung81-group at yahoo.com
Wed Jan 4 13:00:48 CET 2006

you may check your model it may severely distorted.

Yang Ye

----- Original Message ----
From: hnam <mahnam at ibb.ut.ac.ir>
To: gmx-users at gromacs.org
Sent: Wednesday, January 04, 2006 7:20:00 PM
Subject: [gmx-users] mdrun problem

In the name of God
 Hello everyone 
 i constraint one water molecule in active site my protein.
 When I run mdrun with md.mdp ,it says:
 Program mdrun, VERSION 3.3
Source code file: nsgrid.c, line:  226
 Range checking error:
Explanation: During neighbor searching, 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 .. 2744 ]
Please report this to the mailing list (gmx-users at gromacs.org)
 Would you please tell me what  it means.
Thank you very much in  advance
Institute of  Biochemistry  and  Biophysics  (IBB)
Tehran University 
P.O.box 1417614411

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