[gmx-users] Extracting enthalpies during or after MD

lists at jsx.dk lists at jsx.dk
Fri Jun 4 00:35:48 CEST 2010


I am wondering if it is possible to output interaction energies/enthalpies
during an MD simulation between specific groups of atoms.

The energies are all calculated anyways before the forces are calculated,
so I am wondering if there is an option to output those energies to a

I saw someone on the list who had re-coded gromacs to output these
energies, but this resulted in a significant slowdown of the simulation
because he made the code perform output in an inner-loop.

If this is not an option, is there a clever way to get these numbers out
after having run the simulation. Essentially, what I want is to get the
enthalpy, between e.g. a PO4 head-group bead and a C1A tail-bead using the
Martini FF.

Any and all suggestions are welcome!
Best regards,

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