[gmx-users] Extract LJ-14 energy

[Suvardhan Jonnalagadda]

Hi All,

*"GROMACS: VERSION 4.5.5; Precision: single"*
I have performed an md simulation for 1 time step, on a single molecule
with 17 atoms. I want to calculate all the energies (angle, dihedrals,
bonds, 1-4 interactions), and compare. However, I am not able to get the
LJ-14 interactions energy from the '*.edr'* file. When i searched in the
manual, I came across *'gmx enemat'* command.
I gave the following command

*'gmx enemat -f nvt_single.edr -groups groups.dat -lj14'*
In the groups.dat I have entered the molecule name (as in the *.itp  *file).

So, the error and warnings I get after the above command are as follows:









*"   group 16WARNING! could not find group Coul-SR:C16-C16 (16,16)in energy
fileWARNING! could not find group LJ-SR:C16-C16 (16,16)in energy
fileWARNING! could not find group LJ-14:C16-C16 (16,16)in energy fileWill
select half-matrix of energies with 0 elementsLast energy frame read 0
time    0.000            Will build energy half-matrix of 17 groups, 0
elements, over 1 framesSegmentation fault (core dumped)   "*
Is this a bug? or am I missing something?
Also, what does 'LJ(SR)' term in the energies include? In my case, I have
only one molecule. So, what does this LJ short range include?

Thank you,

Best regards,
Vardhan