[gmx-users] Total Energy, g_energy

[Vito GENNA]

Dear GMXusers,

Here I am again with an unresolved problem.
Briefly, in th active site of a system I've run, i have different molecules.
As easily conceivable, I do expect different stabilities in terms of
energy. I am basically interested in getting something similar to Fig. 6 of
https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3192800/figure/pcbi-1002189-g006/
in order to highlight the different stabilities

What I did:
by changing energygrps keyword in the md.mdp (*and maintaining System in
the tc-grps*) I have generated 3 different .tpr
1) energygrps = AET PROTEIN
2) energygrps = BET PROTEIN
3) energygrps = CET PROTEIN
At this point, I have used rerun command with the newly generated .tpr to
get the new ener.edr files.
So far it seems ok.
Now I have two questions:
1) once i run g_enery I get all the possibile combinations of LJ and
Coulombic terms of my energygrps. Great. However, I also get options:
TOT.ENERGY, KINETIC, CONSERVED, POTENTIAL and so on.
Are these referring to the groups declared in my mdp files or, differently,
they refer to the whole system (thus comprising water, ions and so on). The
question rises because if I measure the TOT.ENERGY of my systems they are
almost overlapped!! (altought evidently one of the molecules has very bad
interactions with the active site, and it is ready to depart)

2) which terms (g_energy) should I use/combine to get a potential energy
description of my molecules in my protein (Fig. 6 of the link I have
reported)? I need some quick and qualitative (not FEP et similia)

Thanks in advance for any kind contribution.
I am stuck at this point!

V

-- 

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*Vito Genna, Ph.D*
*EMBO Fellow*

*Postoctoral Researcher*

*Molecular Modeling and Bioinformatics*
*Orozco Lab*

*Institute for Research in Biomedicine (IRB Barcelona)*

*Parc Centific de Barcelona*

*C/ Baldiri Reixac 10-12*
*08028 Barcelona*

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