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

Luca Mollica luca.mollica at ibs.fr
Fri May 21 14:44:04 CEST 2010

Dear Anna,
are you talking about a system "in vacuo" or in solvent ?
If you have placed the protein in water w/o minimizing it before 
solvation, probabily an "in vacuo" minimization could be useful for your 
system before moving into the solvated case. Moreover, are you sure that 
the protein does not have "broken" residue or something like that ? 
Sometimes, the completion of topology creation step goes fine but 
something wrong (on the gromacs side, apart from visualization) with 
sidechains or portion of the proteins that are generated by other 
I do not think it's a ligand problem, BTW.



> 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 alone)
> 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 ligand.
> What do you think about? Could you give me some hint?
> Thank you very much and best regards
> Anna
> __________________________________________________________________
> 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 <mailto: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 
> mosquito"




Luca Mollica
Protein Dynamics and Flexibility by NMR
Institut de Biologie Structurale
41 Rue Jules Horowitz

E-mail: luca.mollica at ibs.fr (lucamollica at gmail.com)

Telephone: +33.438783889


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