[gmx-users] Extract LJ-14 energy

[Suvardhan Jonnalagadda]

Hi,

I am facing the same issue in version 5.1.4 as well.
I have 1-4 interactions in my system (mentioned 'gen-pair' yes in
'forcefield.itp file)

Is there a way to extract the 1-4 interaction energy?

Thank you

On Fri, Dec 20, 2019 at 2:43 PM Mark Abraham <mark.j.abraham at gmail.com>
wrote:

> Hi,
>
> On Thu., 19 Dec. 2019, 18:41 Suvardhan Jonnalagadda, <
> j.su.vardhan at gmail.com>
> wrote:
>
> > Hi All,
> >
> > *"GROMACS: VERSION 4.5.5; Precision: single"*
> >
>
> This software is nearly a decade old and is no longer supported. Please
> update.
>
> 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.
>
>
> The simplest reason would be if the model has none. Or maybe that ancient
> version does something buggy.
>
> When
>
> > i searched in the
> > manual, I came across *'gmx enemat'* command.
> > I gave the following command
> >
>
> That won't help if the data was never in the file.
>
> Mark
>
> *'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
> > --
> > Gromacs Users mailing list
> >
> > * Please search the archive at
> > http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before
> > posting!
> >
> > * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
> >
> > * For (un)subscribe requests visit
> > https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or
> > send a mail to gmx-users-request at gromacs.org.
> >
> --
> Gromacs Users mailing list
>
> * Please search the archive at
> http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before
> posting!
>
> * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
>
> * For (un)subscribe requests visit
> https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or
> send a mail to gmx-users-request at gromacs.org.
>


-- 
*suvardhan*