[gmx-users] calculate avarage and maximum non-bonded energy between energy groups

Tushar Ranjan Moharana tusharranjanmoharana at gmail.com
Mon Aug 24 21:25:20 CEST 2015

Hi everyone,
I want to calculate the average and if possible maximum non-bonded energy
between different energy groups. I used gmx energy whose out put was energy
vs time. I want different energy groups in X axix and energy (average
and/or maximum) in Y axis. A matrix of N X N describing energy (average
and/or maximum) between energy groups is also fine. (where N is number of
energy group).
I tried gmx enemat but it ends with following error

*Opened FOA2_lip_pull.edr as single precision energy fileWill read
groupnames from inputfileRead 2 groupsgroup 0WARNING! could not find group
Coul-SR:Protein-Protein (0,0)in energyfileWARNING! could not find group
LJ-SR:Protein-Protein (0,0)in energy fileWARNING! could not find group
Coul-SR:Protein-Non-protein (0,1)in energyfileWARNING! could not find group
LJ-SR:Protein-Non-protein (0,1)in energy filegroup 1WARNING! could not find
group Coul-SR:Non-protein-Non-protein(1,1)in energy fileWARNING! could not
find group LJ-SR:Non-protein-Non-protein (1,1)in energyfileWill select
half-matrix of energies with 0 elementsLast energy frame read 1400 time
1400.000Will build energy half-matrix of 2 groups, 0 elements, over 1401
framesSegmentation fault (core dumped)*

I tried 4.6.7 version and install GROMACS in debug mode but nothing worked
for me.

Can anybody suggest me something. Little hint will also be helpful.

Thanks a lot in advance.

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

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

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