[gmx-users] Probable bug in 5.0.4 gmx enemat

Tushar Ranjan Moharana tusharranjanmoharana at gmail.com
Fri Aug 14 17:32:06 CEST 2015

Hi friends,
I want to analyze interaction energy between 2 groups of atoms. I use gmx
enemat. However I got following errors.

Opened FOA2_lip_pull.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
WARNING! could not find group LJ-SR:Protein-Protein (0,0)in energy file
WARNING! could not find group Coul-SR:Protein-Non-protein (0,1)in energy
WARNING! could not find group LJ-SR:Protein-Non-protein (0,1)in energy file
group 1WARNING! could not find group Coul-SR:Non-protein-Non-protein
(1,1)in energy file
WARNING! could not find group LJ-SR:Non-protein-Non-protein (1,1)in energy

Will select half-matrix of energies with 0 elements
Last energy frame read 1400 time 1400.000
Will build energy half-matrix of 2 groups, 0 elements, over 1401 frames
Segmentation fault (core dumped)

I am using gromacs5.0.4 version (Quick and dirty installation). In
gromacs4.6 there was bug which used to cause similar problem but latter it
got fixed. I want to know whether it is another bug? What is the solution
for that?

My command line was    gmx enemat -f FOA2_lip_pull.edr  -groups
energy_groups.dat -etot FOA1_lip_push_en.xvg -mean -temp 310

I tried many other combination which includes changing energy_groups.dat
content, analyzing a different .edr file and removing -mean and -temp flags

Please help me to solve this. Thanks for your time and effort.

"A society with free knowledge is better than a society with free food"

Tushar Ranjan Moharana
B. Tech, NIT Warangal
Ph D Student, CCMB

More information about the gromacs.org_gmx-users mailing list