[gmx-users] Extract LJ-14 energy

[Suvardhan Jonnalagadda]

Hi,
Thanks for the reply.
I have included it and rerun my system. Still problem prevails.



On Fri, 20 Dec, 2019, 7:22 AM Bratin Kumar Das, <177cy500.bratin at nitk.edu.in>
wrote:

> Hi
>    You have to mention energygrous in your .mdp file and rerun the
> simulation. The details you'll get in gromacs protein- ligand complex
> tutorial.
>
> On Thu 19 Dec, 2019, 11:11 PM Suvardhan Jonnalagadda, <
> j.su.vardhan at gmail.com> wrote:
>
> > 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
> > --
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