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

Luca Mollica luca.mollica at ibs.fr
Fri May 21 14:46:28 CEST 2010

the problem is not the potential energy, but the force that must converge.
The "inf" there about force and about atom 1 tells me that the computed 
force has problems, indeed.
Which is atom 1 ? Is the protein Nter neutral or charged ? Or is atom 1 
an atom from the ligand ?



> 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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