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.bra...@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.vard...@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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