[gmx-users] Adding urea molecules to lysozyme simulation

Martin Nors Pedersen martin.pedersen at esrf.fr
Thu Sep 3 10:57:24 CEST 2015

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
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?


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