[gmx-users] stepsize too small ... but potential energy negative!

Anna Marabotti anna.marabotti at isa.cnr.it
Fri May 21 14:34:34 CEST 2010

Dear gmx-users,
I tried to minimize my systems formed by a protein obtained by homology
modelling procedure, in one case with a ligand inside, in the other case in
the apo form.
All worked fine until the minimization step: when I launched mdrun, the well
known "stepsize too small..." communication appears. The program worked for
37 steps without producing output energies, and the final report was:
Potential Energy = -6.07e+5 (for the prot+lig); -5.58e+5 (for the protein
Maximum force =                   inf on atom 1
Norm of force =                  inf
I had a look to the gmx-user list archive, but when the "stepsize too small"
error is reported, generally the potential energy is very high. In my case,
the potential energy seems to be correct (it is negative, and the order of
magnitude is similar to that of other systems I studied before). Usually
when I retrieve this error, either the potential energy is very positive and
high, or there are errors in the protein, but I visualized the systems with
VMD and they seem to be correct. It would sound VERY strange if I had the
protein already in a minimum of potential energy!!! Moreover, the same thing
happens in both cases, so I don't think it's a problem related to the
What do you think about? Could you give me some hint?
Thank you very much and best regards
Anna Marabotti, Ph.D.
Laboratory of Bioinformatics and Computational Biology
Institute of Food Science - CNR
Via Roma, 64
83100 Avellino
Phone: +39 0825 299651
Fax: +39 0825 781585
E-mail: amarabotti at isa.cnr.it
Skype account: annam1972
Web site: http://bioinformatica.isa.cnr.it/anna/anna.htm
"If you think you're too small to make a change, try sleeping with a
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