[gmx-users] gmxcheck killed

[Justin Lemkul]

On 1/9/15 5:31 AM, Jennifer Vo wrote:
> 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
> interactions.*
>
> 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.

Only use gmxcheck on one file at a time.  If you want the methods output, use 
gmxcheck -s.  If you want the contents of a given file, just analyze that file.

-Justin

-- 
==================================================

Justin A. Lemkul, Ph.D.
Ruth L. Kirschstein NRSA Postdoctoral Fellow

Department of Pharmaceutical Sciences
School of Pharmacy
Health Sciences Facility II, Room 629
University of Maryland, Baltimore
20 Penn St.
Baltimore, MD 21201

jalemkul at outerbanks.umaryland.edu | (410) 706-7441
http://mackerell.umaryland.edu/~jalemkul

==================================================