[gmx-users] calculating energy between certain groups

Irem Altan irem.altan at duke.edu
Mon May 21 17:35:47 CEST 2018

Thanks. My .mdp file does not contain energy groups, so that was the problem. Given your comments about enemat giving qualitative results, is it possible to get interaction energy between certain groups with gmx energy? I would like to calculate the energy between two protein chains, between solvent and protein, etc. What is the correct way of doing this?


On May 21, 2018, at 8:13 AM, Justin Lemkul <jalemkul at vt.edu<mailto:jalemkul at vt.edu>> wrote:

On 5/20/18 9:49 PM, Irem Altan wrote:
I tried the following:

mdrun -rerun umbrella0.xtc -np cpu -deffnm umbrella0

and also I can verify from the output file that it didn’t use GPUs. However, I still get the same error with gmx enemat:

GROMACS:      gmx enemat, version 2016.3
Executable:   /opt/gromacs/bin/gmx_mpi
Data prefix:  /opt/gromacs
Working dir:  /oasis/scratch/comet/nano3/temp_project/c4_m_4C/rerun
Command line:
  gmx_mpi enemat -f umbrella0.edr

Opened umbrella0.edr as single precision energy file
Will read groupnames from inputfile
Read 2 groups
group 0WARNING! could not find group Coul-SR:Protein-Protein (0,0)in energy file
WARNING! could not find group LJ-SR:Protein-Protein (0,0)in energy file
WARNING! could not find group Coul-SR:Protein-SOL (0,1)in energy file
WARNING! could not find group LJ-SR:Protein-SOL (0,1)in energy file
group 1WARNING! could not find group Coul-SR:SOL-SOL (1,1)in energy file
WARNING! could not find group LJ-SR:SOL-SOL (1,1)in energy file

Will select half-matrix of energies with 0 elements
Last energy frame read 2000 time 20000.000
Will build energy half-matrix of 2 groups, 0 elements, over 2001 frames
Segmentation fault

What could be the problem?

A seg fault almost always indicates buggy behavior, but you need to make sure you specified appropriate energygrps in the .mdp file that created the .tpr and that they are present in the .edr file. Note that you should probably just be using gmx energy to get the time series and statistics. enemat produces a graphical representation (qualitative) whereas energy gives a quantitative description.



Justin A. Lemkul, Ph.D.
Assistant Professor
Virginia Tech Department of Biochemistry

303 Engel Hall
340 West Campus Dr.
Blacksburg, VA 24061

jalemkul at vt.edu<mailto:jalemkul at vt.edu> | (540) 231-3129


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