[gmx-users] calculating energy between certain groups

Justin Lemkul jalemkul at vt.edu
Mon May 21 14:13:52 CEST 2018

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 | (540) 231-3129


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