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

Justin Lemkul jalemkul at vt.edu
Sun Dec 3 23:27:13 CET 2017

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 A. Lemkul, Ph.D.
Assistant Professor
Virginia Tech Department of Biochemistry

303 Engel Hall
340 West Campus Dr.
Blacksburg, VA 24061

jalemkul at vt.edu | (540) 231-3129


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