[gmx-users] Extract LJ-14 energy

[Suvardhan Jonnalagadda]

Hi,
Thanks for the reply. In the log file I could not find any 'LJ14' term, but
'LJ (SR) term is present.

My molecule has 17 atoms, and there are 1-4 interactions.

1.) Is the LJ(SR) term not the same as LJ14, in my case, since I have only
one molecule?

2.) Also, how to see what 1-4 interactions gromacs has considered for the
calculations? When I calculated for the molecule, manually, the 1-4 LJ
contribution is mismatching.

Sorry for late response.

Thanks and regards,

On Sat, 21 Dec, 2019, 7:04 AM Justin Lemkul, <jalemkul at vt.edu> wrote:

>
>
> On 12/20/19 6:07 AM, Suvardhan Jonnalagadda wrote:
> > Hi,
> > Thanks for the reply.
> > I have included it and rerun my system. Still problem prevails.
>
> energrps are not required for LJ 1-4 energies, as these are
> intramolecular and energygrps correspond strictly to intermolecular
> interaction energies.
>
> There is no need for enemat, which in any case is not practical to use
> enemat, just extract the energies with gmx energy. As Mark said, if your
> topology specifies 1-4 interactions, the energy contribution will be
> there. If it's not, there are no 1-4 interactions.
>
> -Justin
>
> >
> >
> > 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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> --
> ==================================================
>
> Justin A. Lemkul, Ph.D.
> Assistant Professor
> Office: 301 Fralin Hall
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>
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