[gmx-users] calculating energy between certain groups

[Irem Altan]

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?

Best,
Irem