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

[João M. Damas]

Hi Berk,

Thanks for your answer. Ok, so tpic should be disregarding that internal
energy and giving me what I said in the first e-mail (intermolecular energy
between the inserted molecule and the rest of the system). The steepest is
not. Still, I'm surprised to get such a big difference from inserting a
molecule with two atoms.

I ran a few more tests to check this out. First of all, I must correct a
previous statement: I used g_energy because I was doing a -rerun when doing
steep. Now I've corrected that and I'm running a real steep with nsteps=0
(that answers your question Javier, I think). I don't get an .edr from that,
so I just use the potential energy output in the log file.

So, I inserted a two atom molecule in time=0 with nsteps=2 (two insertions
in the same frame with different orientations). I got the dumped
conformation with the epot from tpic. From those dumped conformations I ran
the steep I mentioned. I got these results:

           |         tpic
step 0  |  1.82452e+08
step 1  |  1.33190e+08

           |     noligand      |       ligand      |   difference
step 0  |  -3.68255e+04 |  1.86556e+08 | 1.86593e+08
step 1  |  -3.68255e+04 |  1.36063e+08 |   1.361e+08

           |    difference - tpic
step 0  |       4.141e+06
step 1  |       2.910e+06

Why such a discrepancy in the internal energy between the two cases? Since
the inserted molecule is the same, step 0 and step 1 should be equal in the
last calculation, no?

For reference, the same calculation using just a CL- ion:

           |         tpic
step 0  |  1.00584e+07
step 1  |  9.52561e+06

           |     noligand      |       ligand      |   difference
step 0  |  -3.68255e+04 |  1.00217e+07 | 1.00585e+08
step 1  |  -3.68255e+04 |  9.48887e+06 |   9.5257e+06

           |    difference - tpic
step 0  |           100
step 1  |            90

Once again, thank you for your answers, Berk and Javier.

Regards,
João

On Fri, Mar 4, 2011 at 8:30 AM, Berk Hess <hess at cbr.su.se> wrote:

> Hi,
>
> 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
> results.
>
>  Berk
>
> 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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-- 
João M. Damas
PhD Student
Protein Modelling Group
ITQB-UNL, Oeiras, Portugal
Tel:+351-214469613
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