[gmx-users] Step.pdb generated during energy minimization

[Justin Lemkul]

On 12/2/17 11:48 PM, vijayakumar gosu wrote:
> Hi gromacs users,
>
> I am performing simulations of protein and RNA complex using gromacs 5.14.
> However during gromacs energy minimization seems to be converged and output
> em.gro files are generated.  however some step.pdb files are generated
> during energy minimization. Total number of atoms are 308312
>
> EM output
> writing lowest energy coordinates.
>
> Steepest Descents converged to Fmax < 1000 in 3621 steps
> Potential Energy  = -4.9057965e+06
> Maximum force     =  8.3348792e+02 on atom 17333
> Norm of force     =  7.2829952e+00
>
>
> I have performed subsequent equilibriation and production for 100 ns,
> simulation data seems fine. I did not find any other problems during
> equilibriation and production run.
>
> please suggest me if there is anything goes wrong?

If EM completes successfully, it shouldn't be a problem. The step*.pdb 
are from unstable frames, but if EM proceeds past them, likely it is OK. 
These should never be produced during stable dynamics, though.

-Justin

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Justin A. Lemkul, Ph.D.
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