[gmx-users] genbox solvate insert_molecules

Justin Lemkul jalemkul at vt.edu
Wed Jun 18 19:58:00 CEST 2014

On 6/18/14, 1:52 PM, Soren Wacker wrote:
> Hi,
> when I start genbox with GMX5.x, I get the message:
> This tool has been removed from Gromacs 5.0. Please see
>    http://www.gromacs.org/Documentation/How-tos/Tool_Changes_for_5.0
> at this website it is stated:
> "This tool has been split to gmx solvate and gmx insert-molecules."
> Apparently, these tools do not exist on my system. Should they be compiled by default?
> How can I generate these files if not?

There is only one "gmx" binary that is installed in 5.0.  Old tool names link to 
it and all commands (like "gmx solvate") are invoked as modules of gmx.  Try 
"gmx solvate -h" and see if it works.  It is installed by default.



Justin A. Lemkul, Ph.D.
Ruth L. Kirschstein NRSA Postdoctoral Fellow

Department of Pharmaceutical Sciences
School of Pharmacy
Health Sciences Facility II, Room 601
University of Maryland, Baltimore
20 Penn St.
Baltimore, MD 21201

jalemkul at outerbanks.umaryland.edu | (410) 706-7441


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