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

[Tushar Ranjan Moharana]

Hi Justin,
Thanks for your precious advice. You replied that "I would agree with
Vitaly that this is really not a useful quantity. It is force
field-specific and not necessarily anything to do with thermodynamics or
free energy." did you refer to maximum energy or average energy or both.

You also adviced to use a terminal that allows scrolling. Now I am able to
scroll in my terminal. However I read in many places about gmx enemat which
can extract energy matrix. How ever in my case it gives following error.

Read 40 groups
group 0WARNING! could not find group Coul-SR:VAL171    -VAL171     (0,0)in
energy file
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
WARNING! could not find group Coul-SR:VAL171    -VAL174     (0,2)in energy
file
WARNING! could not find group LJ-SR:VAL171    -VAL174     (0,2)in energy
file
WARNING! could not find group Coul-SR:VAL171    -VAL187     (0,3)in energy
file
WARNING! could not find group LJ-SR:VAL171    -VAL187     (0,3)in energy
file
WARNING! could not find group Coul-SR:VAL171    -ILE203     (0,4)in energy
file
WARNING! could not find group LJ-SR:VAL171    -ILE203     (0,4)in energy
file
WARNING! could not find group Coul-SR:VAL171    -TYR204     (0,5)in energy
file

...........

group 38WARNING! could not find group Coul-SR:ODE    -ODE     (38,38)in
energy file
WARNING! could not find group LJ-SR:ODE    -ODE     (38,38)in energy file
WARNING! could not find group Coul-SR:ODE    -ODA (38,39)in energy file
WARNING! could not find group LJ-SR:ODE    -ODA (38,39)in energy file
group 39
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)


I read from GROMACS user mailing list where you have suggested someone to
install GROMACS in debug mode or use GROMACS-4.6.5. I have tried both but
nothing worked for me. am I doing any mistake? My energygrp-excl is empty
as it is not supported by Verlet. In the above case what ever group was not
found by gmx enemat was read by gmx energy and gives output in the same
.edr file.


Thank you 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