[gmx-users] minimization is not converging

Justin Lemkul jalemkul at vt.edu
Thu Sep 6 16:22:19 CEST 2018

On 9/6/18 10:09 AM, Bratin Kumar Das wrote:
> Respected Dr. Justin
>                                       To avoid the complicacy I solvated
> only the protein pdb in a pbc box and tried for minimizatin. There also
> minimization is not converging. Sir, till now I learned to carry out
> protein ligand system md simulation successfully. I tried all possible ways
> to simulate the my membrane protein system. I failed. Is it possible that
> the PDB file itself have some serious issue with its coordinates. the
> structure refinement is required may be.

It may, and I have already suggested a few things for you to check. 
Please do so.

If you can provide more specific diagnostics of what is happening, 
someone on this list might be able to suggest something. What you've 
provided thus far is a generic instability that no one can diagnose. 
Investigate the structure, check for pdb2gmx warnings, follow the 
diagnostics I've already suggested, and report back with specific 
observations, a PDB code, and exact errors or warnings you get from any 
program if you need further help.



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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