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

vijayakumar gosu vijayakumargosu at gmail.com
Sun Dec 3 05:48:14 CET 2017

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?


Vijayakumar Gosu  Ph.D
Post Doctoral Fellow
The Animal Genomics and Breeding Center
Chonbuk National University
Tel: +821073270537

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