[gmx-users] Adding urea molecules to lysozyme simulation

Justin Lemkul jalemkul at vt.edu
Thu Sep 3 14:07:38 CEST 2015

On 9/3/15 4:57 AM, Martin Nors Pedersen wrote:
> Thank you for the reply Justin!
> I'm sorry for being so naive, but I still cannot get it to work.
> Trying to follow the procedure described in you link, I got the following message:
> ______________________________
> GROMACS:      gmx genbox, VERSION 5.0.4
> Executable:   /sware/exp/gromacs/5.0.4/bin/gmx_mpi
> Library dir:  /sware/exp/gromacs/5.0.4/share/gromacs/top
> Command line:
>    gmx_mpi genbox -f lysBox.gro -o lysUrea.gro -ci urea.gro -nmol 300
> This tool has been removed from Gromacs 5.0. Please see
>    http://www.gromacs.org/Documentation/How-tos/Tool_Changes_for_5.0
> for ideas how to perform the same tasks with the new tools.
> ______________________________
> The link in the software message above mentions that "insert-molecules" should
> be used instead, but that is the library/package that I could not get to work
> yesterday :S
> Can anyone help?

The syntax is identical, just replace "genbox" with "insert-molecules."  The 
functionality has literally just been split from genbox, which was trying to do 
too many things for a simple program.  Your command wasn't working before 
because you were trying to add urea after water, which won't work.



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

Department of Pharmaceutical Sciences
School of Pharmacy
Health Sciences Facility II, Room 629
University of Maryland, Baltimore
20 Penn St.
Baltimore, MD 21201

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


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