[gmx-users] Probable bug in 5.0.4 gmx enemat
Tushar Ranjan Moharana
tusharranjanmoharana at gmail.com
Thu Aug 27 13:12:12 CEST 2015
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
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