[gmx-users] please help clarifying units for potential energy and enthalpy from gmx energy

[Mark Abraham]

Hi,

I'm not sure, but I think David van der Spoel implemented these, so perhaps
we should invite his input specifically.

Mark

On Thu, Jun 1, 2017 at 5:44 PM Christopher Neale <
chris.neale at alum.utoronto.ca> wrote:

> I am now presuming that the enthalpy is reported in kJ/mol where /mol
> means "per mole of simulation unit cells". That seems fine to me. I still
> think it's strange that the potential energy, but not the enthalpy, output
> by gmx energy is affected by the -nmol option, but perhaps that's for some
> reason the desired behaviour.
>
> ________________________________
> From: gromacs.org_gmx-users-bounces at maillist.sys.kth.se <
> gromacs.org_gmx-users-bounces at maillist.sys.kth.se> on behalf of
> Christopher Neale <chris.neale at alum.utoronto.ca>
> Sent: 30 May 2017 23:25:46
> To: Discussion list for GROMACS users
> Subject: [gmx-users] please help clarifying units for potential energy and
> enthalpy from gmx energy
>
> Dear Users:
>
>
> I am trying to figure out what “potential energy” and “enthalpy” really
> mean in the output from gmx energy. It took me a while to realize that even
> when the (more hidden than it should be) option -nmol is not used and
> therefore is set to its default value of 1, the .xvg output indicates units
> of kJ/mol for the potential energy, when in that default case it is likely
> reporting simply kJ, or perhaps kJ/unit cell.
>
>
> But then what about the “enthalpy”? It also is given units of kJ/mol in
> the .xvg output from gmx energy, but that numerical output is not affected
> at all by the value of -nmol.
>
>
> I show some output below to prove scaling of the output “potential energy”
> but no the “enthalpy” with the -nmol option to gmx energy, but that is just
> to show the change with different options to gmx energy on the same .edr
> file.
>
>
> Thank you for the help.
>
> Chris.
>
>
> ## without -nmol (default to 1)
>
>
> # Command line:
>
> #   gmx energy -f FEMSMNM.edr -o a.xvg
>
> # gmx energy is part of G R O M A C S:
>
> #
>
> # GRowing Old MAkes el Chrono Sweat
>
> #
>
> @    title "GROMACS Energies"
>
> @    xaxis  label "Time (ps)"
>
> @    yaxis  label "(kJ/mol)"
>
> @TYPE xy
>
> @ view 0.15, 0.15, 0.75, 0.85
>
> @ legend on
>
> @ legend box on
>
> @ legend loctype view
>
> @ legend 0.78, 0.8
>
> @ legend length 2
>
> @ s0 legend "Potential"
>
> @ s1 legend "Enthalpy"
>
>     0.000000  -555356.062500  -425480.937500
>
>     0.200000 <020-00%2000>  -530695.812500  -415548.406250
>
>     0.400000  -528639.750000  -410765.750000
>
>     0.600000  -527722.500000  -407132.125000
>
>     0.800000  -526586.687500  -404519.687500
>
>     1.000000  -526814.125000  -402872.875000
>
>     1.200000  -525852.625000  -401044.656250
>
>     1.400000  -525089.250000  -399389.187500
>
>     1.600000  -524979.625000  -398347.593750
>
>     1.800000  -524312.500000  -396957.187500
>
>     2.000000  -524930.062500  -396691.562500
>
>
>
>
> # Command line:
>
> #   gmx energy -f FEMSMNM.edr -o b.xvg -nmol 100
>
> # gmx energy is part of G R O M A C S:
>
> #
>
> # GROwing Monsters And Cloning Shrimps
>
> #
>
> @    title "GROMACS Energies"
>
> @    xaxis  label "Time (ps)"
>
> @    yaxis  label "(kJ/mol)"
>
> @TYPE xy
>
> @ view 0.15, 0.15, 0.75, 0.85
>
> @ legend on
>
> @ legend box on
>
> @ legend loctype view
>
> @ legend 0.78, 0.8
>
> @ legend length 2
>
> @ s0 legend "Potential"
>
> @ s1 legend "Enthalpy"
>
>     0.000000  -5553.560547  -425480.937500
>
>     0.200000 <020-00%2000>  -5306.958008  -415548.406250
>
>     0.400000  -5286.397461  -410765.750000
>
>     0.600000  -5277.225098  -407132.125000
>
>     0.800000  -5265.866699  -404519.687500
>
>     1.000000  -5268.141113  -402872.875000
>
>     1.200000  -5258.526367  -401044.656250
>
>     1.400000  -5250.892578  -399389.187500
>
>     1.600000  -5249.796387  -398347.593750
>
>     1.800000  -5243.125000  -396957.187500
>
>     2.000000  -5249.300781  -396691.562500
> --
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