[gmx-users] gmxcheck killed

Jennifer Vo quyviolet at gmail.com
Fri Jan 9 11:31:32 CET 2015

Dear All,
My command was:
*"gmxcheck_mpi -f md-1.trr -n index.ndx -s1 em-1.tpr -c md-1.gro -e
md-1.edr -m md1-gmxcheck.txt"*

The output "md1-gmxcheck.txt" content was:

*\section{Methods}\subsection{Simulation system}A system of 70256 molecules
(1087816 atoms) was simulated.*

*\subsection{Simulation settings}A total of 0.5 ns were simulated with a
time step of 1 fs.Neighbor searching was performed every 1 steps.The PME
algorithm was used for electrostatic interactions.with a cut-off of 1 nm.A
reciprocal grid of 200 x 200 x 200 cells was used with 4th order B-spline
interpolation.A single cut-off of 1 was used for Van der Waals

There was a list of error
*"Distance between atoms 956362 and 956363 is 0.098, should be 0.094"*
before the *"Reading frame       4 time    4.000...."* was running and
ending as "*killed*"
It seems there are many problems here but I don't know where the begining
of error.
I really appreciate for any help.

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