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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