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
server.
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@gromacs.org)
-------------------------------------------------------
What does it mean and how to go about correcting it? Thanks in advance.
Venks
--
Venky Krishnamani
Graduate Student,
Dr. Janos K. Lanyi Lab
Univerisity of California, Irvine
Irvine, CA
(949) 202-9466
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