[gmx-developers] tpic run option - potential energy meaning

Berk Hess hess at cbr.su.se
Fri Mar 4 09:30:31 CET 2011


The energies reported by tpi and tpic are only the interaction energy of
the inserted
molecule with the rest of the system. If your inserted molecule has
intra molecular
energy terms these will not enter into the reported energies, whereas
such contributions
would appear in the difference you determined by subtracting the two


On 03/04/2011 03:31 AM, João M. Damas wrote:
> Dear all,
> 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 = enerd->term[F_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 kJ/mol.
> Thanks in advance.
> Regards,
> João
> -- 
> João M. Damas
> PhD Student
> Protein Modelling Group
> ITQB-UNL, Oeiras, Portugal
> Tel:+351-214469613

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