[gmx-users] problem regarding grompp

kinshuk at chem.iitb.ac.in kinshuk at chem.iitb.ac.in
Sun Jan 20 04:57:54 CET 2008

 Thanks for giving me insight to resolve the problem regarding grompp.
Now i came across new problem regarding energy minimization
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=
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.
For getting insight about i will be thankful to you.

> kinshuk at chem.iitb.ac.in wrote:
>> Hi all,
>>  I have been trying to simulate peptide (octa alanine). In genbox i have
>> inserted 40 molecule of guanidium ion & 800 water molecule (by -ci &
>> maxsol option in gromacs 3.3.3)then again with genbox i added 40
>> molecules of thiocynate ion & 80 water molecules as above mentioned way.
>> When i tried to do grompp for energy minimization i was encountered with
>> many warning listed below though i have included the *.itp files of both
>> ions in the topology *.top file of peptide.I need some insight about
>> this
>> so that i can resolve this problem.
>> I have attached the em.mdp file along with this mail.
> This is not the problem, but your T-coupling groups aren't useful. See
> http://wiki.gromacs.org/index.php/thermostats
>> If i will be getting help i'll be thankful for you.
> The order of molecules in your .top files [ molecules ] section probably
> doesn't match the order of molecules in your structure file. See chapter
> 5 of the GROMACS manual if you don't understand this.
> Mark
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