[gmx-users] Re: Problem with minimizing the energy of the solvated system

Justin A. Lemkul jalemkul at vt.edu
Thu Jul 5 23:57:53 CEST 2012

On 7/5/12 5:51 PM, jonas87 wrote:
> Protein-water.pdb has the following line:
> CRYST1   75.324   75.324   75.324  60.00  60.00  90.00 P 1           1
> But after adding the NA/CL ions with genion the CRYST1 line is missing
> entirely from the output file protein-solvated.pdb
> Could this be because of the bug u mentioned?

Sounds about right.

> I'm using the latest version of gromacs, that means this bug was
> reintroduced?

Likely it was not fully fixed; I recall a change to editconf, but maybe genion 
needs a look as well.

> So it is ok to always output to .gro instead of .pdb?




Justin A. Lemkul, Ph.D.
Research Scientist
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu | (540) 231-9080


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