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

[Christopher Neale]

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  -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  -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