[gmx-users] minimization is not converging

Justin Lemkul jalemkul at vt.edu
Thu Sep 6 15:54:04 CEST 2018

On 9/6/18 9:51 AM, Bratin Kumar Das wrote:
> Respected Dr Justin,
>                                       I took one membrane protein pdb file
> and converted it to .gro using pdb2gmx. Next I builded and packed the POPC
> phospholipids bylayer using vmd membrane builder plugin. Subsequently I
> solvated the system in vmd only. The entire system was converted to .gro
> and all the water molecules and POPC molecules making bad contacts are
> deleted. I added ions to nutralize the system in gromacs using genion.
> Prior to that all the POPC topoloy properly included in topol.top. prior to
> energy minimization all the steps ran with out fatal error. I followed the
> procidure explained in gromacs tutorial. Evrey cases the same error is
> coming during minimization.

It's not worth moving on to a complicated membrane system when you said 
the protein itself does not minimize properly. Solve the easier problem 
first and work with just the protein. Only when you understand why that 
was unstable should you move on to the membrane system.



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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