[gmx-users] Probable bug in 5.0.4 gmx enemat

[Tushar Ranjan Moharana]

Hi Mark,
Thanks for your reply.

My command line in GROMACS-5.0.4 was :
gmx enemat -f FOB1_lip_push_en.edr -groups energy_groups.dat  -etot
activesite_energy.xvg

and other version was
g_enemat -f FOB1_lip_push_en.edr -groups energy_groups.dat  -etot
activesite_energy.xvg

When I use gmx energy and choose the number for the corresponding energy
terms for which the warning was generated, I got the output, which indicate
that those energy terms are there in the energy group. For example when I
use
gmx enemat -f FOB1_lip_push_en.edr -groups energy_groups.dat  -etot
activesite_energy.xvg

I got many warnings like

WARNING! could not find group LJ-SR:VAL171    -VAL171     (0,0)in energy
file
WARNING! could not find group Coul-SR:VAL171    -MET173     (0,1)in energy
file
WARNING! could not find group LJ-SR:VAL171    -MET173     (0,1)in energy
file

and finally

Will select half-matrix of energies with 2 elements
Last energy frame read 2000 time 2000.000
Will build energy half-matrix of 40 groups, 2 elements, over 2001 frames
Segmentation fault (core dumped)

When I use
 gmx energy -f FOB1_lip_push_en.edr -ravg

and chose 49 52 53 0 got following output

Energy                      Average   Err.Est.       RMSD  Tot-Drift
-------------------------------------------------------------------------------
LJ-SR:VAL171-VAL171         1.63195       0.21    3.18617    0.92525
(kJ/mol)
Coul-SR:VAL171-MET173      0.300122       0.19    1.12586   -1.23602
(kJ/mol)
LJ-SR:VAL171-MET173        -3.83441      0.055   0.839933  -0.142762
(kJ/mol)

You may access my  .edr file .tpr and groups file with the following links
respectively.
https://www.dropbox.com/s/kv8pjcvxdl6f2gr/FOB1_lip_push_en.edr?dl=0
https://www.dropbox.com/s/y5pddabpndmhdq8/FOB1_lip_push_en.tpr?dl=0
https://www.dropbox.com/s/y9ia804dh0766pe/energy_groups.dat?dl=0

Thanks alot for your time and consideration.

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

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