[gmx-users] g_energy output

lists at jsx.dk lists at jsx.dk
Thu Jul 1 20:49:28 CEST 2010

Dear all,

I have run a CG-MD simulation and output energies of different energy groups.
When I run g_energy to get some of the energy terms out I input the number
of molecules in my system -nmol "X" (X = Y number of water molecules
(beads) + Z number of proteins + W number of lipids), to make sure that I
get the correct value of kJ/mol.

Firstly, I am wondering if the number of water molecules (Y) should be the
number of beads, or the number of real water molecules it corresponds to,
that is multiplied by 4?
If I use the number of beads, then the number of molecules gets skewed
because the number of molecules for lipids (W) and protein (Z) even after
coarse-graining is still the same...

Secondly, the results puzzle me a bit. Changing the -nmol number results
in only the bonded energy changing. Is this correct? The remaining terms
(LJ, Coul) stay the same...

I am running gromacs 4.0.7

Kind regards,
Jesper Soerensen

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