[gmx-users] energygrps interactions are 0 for water

Julian Michalowsky j.michalowsky at gmail.com
Thu Sep 17 19:00:29 CEST 2015


I have a problem regarding the calculation of interaction energies using
gmx energy and the energygrps parameter in the mdp file. My mdp file
includes the line

energygrps = Ion OW

Whenever I calculate the LJ-SR and Coul.-SR energy terms between OW
and any other energy group, the result is just zero. I am using an
index file during preprocessing that defines OW as a group and also tried
SOL and Water as energygrps in the mdp file.

I originally used this with a custom force field, but encountered the same
problem during a test run using the gromos54a7.ff from the default top

The system is a simple electrolyte solution (NaCl in water). I use a python
script to set up the initial gro file. Ions are referred to as NA, CL in
both gro
and top file (not NA+ or CL-, if that makes any difference). The top file
includes the respective forcefield.itp, ions.itp and spce.itp topologies via
the #include statement using absolute paths. Gromacs version is 5.0.

I also tried inserting the ions into a box with water using gmx genion. The
results are the same: Ion-Ion interactions are present and non-zero, but
Ion-SOL, SOL-SOL etc. are zero. The problem arises using various temperature
and pressure coupling algorithms. Apart from that, the simulations seem to
run smoothly and not doing exceptionally weird things, even reproduce

I am unable to grasp the source of the issue here, so if you can help, any
input is welcome. Presumably it's just a mistake regarding input on my part,
but I have been trying to solve this problem for quite some time now, so I'm
writing to the mailing list.

Thanks in advance and kind regards,
Julian Michalowsky

More information about the gromacs.org_gmx-users mailing list