[gmx-users] Probable bug in 5.0.4 gmx enemat

Tushar Ranjan Moharana tusharranjanmoharana at gmail.com
Fri Aug 21 17:13:23 CEST 2015

Hi Mark,
As per your suggestion I have tried 4.6.7 version and also installed
gromacs in debug mode. However that didn't help. I got the same error as

*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  file  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  file  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  file  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)*

When I use g_energy I was prompt to choose which energy I want as shown

2505  LJ-SR:MET24-THR177                 2506
2507  LJ-14:MET24-THR177                 2508
2509  LJ-SR:MET24-ASP178                 2510
2511  LJ-14:MET24-ASP178                 2512
2513  LJ-SR:MET24-GLN184                 2514
2515  LJ-14:MET24-GLN184                 2516
2517  LJ-SR:MET24-ALA190                 2518
2519  LJ-14:MET24-ALA190                 2520
2521  LJ-SR:MET24-ALA191                 2522
2523  LJ-14:MET24-ALA191                 2524  Coul-SR:MET24-ALA194

and when I choose a number and 0 it shows

*Statistics over 1000001 steps [ 0.0000 through 2000.0000 ps ], 1 data
setsAll statistics are over 10001 pointsEnergy
Average   Err.Est.       RMSD
-0.150913       0.11    0.43633   0.017812  (kJ/mol)*

Which seems to be correct. But then my question is why gmx enemat is giving
error and what is the solution for that. I want to calculate the average
non-bonded energy between various energy groups. gmx energy is giving me a
particular energy between 2 group as a function of time.

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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