[gmx-users] problem regarding grompp

Mark Abraham Mark.Abraham at anu.edu.au
Sun Jan 20 06:02:45 CET 2008

kinshuk at chem.iitb.ac.in wrote:
>  Thanks for giving me insight to resolve the problem regarding grompp.
> Now i came across new problem regarding energy minimization

Please start a new email thread for a new problem. The subject line is 
your best chance to attract someone who can help you, so make it 
succint, relevant and informative.

> MDRUN(mdrun)step while giving this command to command prompt.
> {mdrun -v -s em.tpr -o em.trr -e em.edr -c after_em.gro -g emlog.log }
> I came across this problem which i am mentioning below.
> Reading file em.tpr, VERSION 3.3.1 (single precision)
> Loaded with Money
> Back Off! I just backed up em.edr to ./#em.edr.2#
> Steepest Descents:
>    Tolerance (Fmax)   =  1.00000e+02
>    Number of steps    =         4000
> -------------------------------------------------------1.31850e+12, atom=
> 1924
> 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 .. 216 ]
> Please report this to the mailing list (gmx-users at gromacs.org)
> -------------------------------------------------------
> What should be problem? I am attaching  emergy minimization em.mdp file.

This is symptomatic of the kinds of problems discussed here... 

Because grompp returned you a .tpr file, your topology may have been 
well-formed. You should run grompp again and pay particular attention to 
any warnings it gives you. Even if it doesn't warn you about anything, 
the odds are excellent that despite being well-formed grammatically, the 
contents of your .top file lead to nonsense physics. Then large force on 
atoms can cause the above symptoms in EM.

You should check your topology carefully, consulting with Chapter 5 of 
the manual where you need to. Break the structure & topology up into 
manageable chunks, and try an EM on an isolated molecule of each type to 
  see which bit of the topology is broken.


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