[gmx-users] tpic run option - potential energy meaning
João M. Damas
jmdamas at itqb.unl.pt
Fri Mar 4 03:31:14 CET 2011
I have some questions about the energy calculated with the tpic integrator
implemented in gromacs.
I've been using the GMX_TPI_DUMP and -debug options as well as looking into
the code in order to figure this out.
At some point, in the do_tpi function, the do_force function is called to do
an energy calculation, with the objective of getting a epot (epot =
My question is what is this epot? I'm guessing it is the difference between
the intermolecular energy of the state without the inserted molecule and the
intermolecular energy of the state with the inserted molecule (which in this
case would mean just the lennard-jones interactions). Am I right?
I started doubting the meaning of this energy when I did the following test:
with the dumped structure of the system with the inserted molecule and the
structure of the system without the molecule, I ran a single steepest
descent calculation to determine the potential energy for each one, and
calculated the diference between them (even with g_energy), and the value
was different from the one that was output in the dumped structure and debug
mode (the epot in do_tpi). The values: 1.86593e+08 (for my test)
vs. 182452256.000000 (of epot dumped from tpic), a difference of 4.14074e+06
Thanks in advance.
João M. Damas
Protein Modelling Group
ITQB-UNL, Oeiras, Portugal
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