[gmx-users] tpic run option - potential energy meaning
JAVIER CEREZO BASTIDA
jcb1 at um.es
Fri Mar 4 17:37:15 CET 2011
I thought that the meaning of "epot" is the one you point out in your
mail. So, I'm also a surprised about your test.
The first thing that came to me mind is on the way you calculate the
energy with a "single" steepest descent step. In your mdp file, did
you use "nsteps=1" or "nsteps=0"? The first involves one optimization
step while the second none of them. You'll probably took care of it
but just to check.
"João M. Damas" <jmdamas at itqb.unl.pt> escribió:
> 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 =
> 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
> PhD Student
> Protein Modelling Group
> ITQB-UNL, Oeiras, Portugal
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