[gmx-users] Extract LJ-14 energy

[Mark Abraham]

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
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