Hi Berk,<div><br></div><div>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.</div>
<div><br></div><div>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.</div>
<div><br></div><div>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:</div>
<div><br></div><div> | tpic</div><div>step 0 | 1.82452e+08</div><div>step 1 | 1.33190e+08</div><div><br></div><div><div> | noligand | ligand | difference</div><div>step 0 | -3.68255e+04 | 1.86556e+08 | 1.86593e+08</div>
<div>step 1 | -3.68255e+04 | 1.36063e+08 | 1.361e+08</div></div><div><br></div><div><div> | difference - tpic</div><div>step 0 | 4.141e+06</div><div>step 1 | 2.910e+06</div></div><div><br>
</div>
<div>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?</div><div><br></div><div>For reference, the same calculation using just a CL- ion:</div>
<div><br></div><div><div> | tpic</div><div>step 0 | 1.00584e+07</div><div>step 1 | 9.52561e+06</div><div><br></div><div><div> | noligand | ligand | difference</div><div>
step 0 | -3.68255e+04 | 1.00217e+07 | 1.00585e+08</div><div>step 1 | -3.68255e+04 | 9.48887e+06 | 9.5257e+06</div></div><div><br></div><div><div> | difference - tpic</div><div>step 0 | 100</div>
<div>step 1 | 90</div></div></div><div><br></div><div>Once again, thank you for your answers, Berk and Javier.</div><div><br></div><div>Regards,</div><div>Joćo</div><div><br><div class="gmail_quote">On Fri, Mar 4, 2011 at 8:30 AM, Berk Hess <span dir="ltr"><<a href="mailto:hess@cbr.su.se">hess@cbr.su.se</a>></span> wrote:<br>
<blockquote class="gmail_quote" style="margin:0 0 0 .8ex;border-left:1px #ccc solid;padding-left:1ex;">Hi,<br>
<br>
The energies reported by tpi and tpic are only the interaction energy of<br>
the inserted<br>
molecule with the rest of the system. If your inserted molecule has<br>
intra molecular<br>
energy terms these will not enter into the reported energies, whereas<br>
such contributions<br>
would appear in the difference you determined by subtracting the two<br>
results.<br>
<br>
Berk<br>
<div><div></div><div class="h5"><br>
On 03/04/2011 03:31 AM, Joćo M. Damas wrote:<br>
> Dear all,<br>
><br>
> I have some questions about the energy calculated with the tpic<br>
> integrator implemented in gromacs.<br>
><br>
> I've been using the GMX_TPI_DUMP and -debug options as well as looking<br>
> into the code in order to figure this out.<br>
><br>
> At some point, in the do_tpi function, the do_force function is called<br>
> to do an energy calculation, with the objective of getting a epot<br>
> (epot = enerd->term[F_EPOT]).<br>
><br>
> My question is what is this epot? I'm guessing it is the difference<br>
> between the intermolecular energy of the state without the inserted<br>
> molecule and the intermolecular energy of the state with the inserted<br>
> molecule (which in this case would mean just the lennard-jones<br>
> interactions). Am I right?<br>
><br>
> I started doubting the meaning of this energy when I did the following<br>
> test: with the dumped structure of the system with the inserted<br>
> molecule and the structure of the system without the molecule, I ran a<br>
> single steepest descent calculation to determine the potential energy<br>
> for each one, and calculated the diference between them (even with<br>
> g_energy), and the value was different from the one that was output in<br>
> the dumped structure and debug mode (the epot in do_tpi). The<br>
> values: 1.86593e+08 (for my test) vs. 182452256.000000 (of epot dumped<br>
> from tpic), a difference of 4.14074e+06 kJ/mol.<br>
><br>
> Thanks in advance.<br>
><br>
> Regards,<br>
> Joćo<br>
><br>
> --<br>
> Joćo M. Damas<br>
> PhD Student<br>
> Protein Modelling Group<br>
> ITQB-UNL, Oeiras, Portugal<br>
> Tel:+351-214469613<br>
<br>
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</font></blockquote></div><br><br clear="all"><br>-- <br>Joćo M. Damas<br>PhD Student<br>Protein Modelling Group<br>ITQB-UNL, Oeiras, Portugal<br>Tel:+351-214469613<br>
</div>