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

Justin A. Lemkul jalemkul at vt.edu
Mon May 24 13:06:47 CEST 2010

Anna Marabotti wrote:
> Dear Luca, dear all,
> thank you for your hints. I made some trials with my systems and these are
> my answers to your questions:
> - my system is a protein (with or w/o ligand) in solvent (water SPC).
> Following your suggestions, I tried to perform an EM on the protein w/o
> ligand after the editconf step (i.e. I created the topology with pdb2gmx,
> created a cubic box with editconf, then I used grompp+mdrun to perform EM).
> I received the same error: the minimization starts, performs 37 steps, then
> stops with the "stepsize too small...." communication. The energy in this
> case is -3.06e+4 (one order of magnitude higher than the solvated system)
> but still negative, and the maximum force is still "inf on atom 1". So
> minimizing in vacuo does not help to solve the problem. This atom 1 is the
> Nter of the protein, it is belonging to a Ser and I did not charge it
> explicitly with pdb2gmx (i.e. I did not use the flag -ter) but it is bound
> to 3 H in the .gro file.

Were there any messages from pdb2gmx when you produced your topology?  How large 
is your box?  What force field are you using?

> - If I look at the protein with VMD or other visualizing tools, it seems to
> me that no major problems are present on the structure. In particular, atom
> 1 is not "broken" or something similar, I can't see no "aberrations". I
> don't know how to check if something goes wrong apart from visualization, do
> you know some tools that could automatically check the file? To the best of
> my knowledge, gmxcheck performs checks only on trajectories, or can I use it
> also on single structures?

There is no tool for troubleshooting this kind of problem.  gmxcheck will 
inspect the integrity of a file (including single structures), but will not 
magically tell you what's wrong with it :)

> - I also tried to continue anyway after the minimization step with the PR MD
> in NVT, but it did not start because of a lot of LINCS error. It suggests me
> that some distortions are present in my structure, but if I cannot minimize
> it, how to relieve this problem?

If a system does not minimize, any further steps will be futile.


>         G96Bond       G96Angle    Proper Dih.  Improper Dih.          LJ-14
>     2.40716e+03    1.23569e+03    6.85831e+02    8.70819e+01   2.11992e-314
>      Coulomb-14        LJ (SR)        LJ (LR)   Coulomb (SR)   Coul. recip.
>    2.11992e-314   -2.19860e+03   -1.52663e+02   -6.70307e+03   -2.59368e+04
>       Potential Pressure (bar)
>    -3.05754e+04            nan

The fact that your LJ-14 and Coulomb-14 energies are essentially numerical 
infinity (!) suggests some very bad underlying problem.  Hard to say at this 
point what it is though.

Other useful information would be the actual .mdp file you're using, and answers 
to my questions above.



Justin A. Lemkul
Ph.D. Candidate
ICTAS Doctoral Scholar
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu | (540) 231-9080


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