[gmx-users] Energy too high for free energy

Ing. Vojtěch Spiwok Vojtech.Spiwok at vscht.cz
Thu May 29 16:32:00 CEST 2003

Hi gromacs users / developers

I'm trying to estimate a free energy from MD of the
complex of large protein (> 1000 AA) and small ligand
in order to compare free energies of two binding modes
which are different in conformation but same in topology.
This system is huge (> 80 000 atoms) and the potential
energy in absolute magnitude is high (- 10^6 kJmol-1).
When trying g_energy i recieve "inf" instead of free
energy estimate. I would like to ask wether this is due
to the fact that E/kT is too low so e^(E/kT) is close to
zero (out of precision of calculation) ? Than it would be
possible to calculate it from the output file. Is it correct
to set potential energy (# 9 in g_energy menu) for such
free-energy estimation ?
Thank you very much for previous answers.

Vojtech Spiwok
ICT Prague

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