[EMAIL PROTECTED] 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 ([email protected])
-------------------------------------------------------
What should be problem? I am attaching emergy minimization em.mdp file.
This is symptomatic of the kinds of problems discussed here...
http://wiki.gromacs.org/index.php/blowing_up
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.
Mark
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