2011/5/23 Jesper Sørensen <lists.jsx.dk>
> Hi,
>
> I have a quick question about the results of an entropy calculation...
> mostly for clarification
>
> The units are reported in:
> |All units are reported in kcal/mole.
> |All entropy results have units kcal/mole (Temperature is 298.15 K).
>
> The result is:
> DELTA S total= -53.1557 +/- 7.5856
>
> 1) Does this mean that the result is in fact "T * DELTA S total" ?
>
Yes.
> 2) Or do I still need to multiply this result with the temperature?
> 3) In case 1 is the correct answer, is there a way to change the
> temperature
> used to not be 298.15 K?
>
Yes, but it's not quite as straight-forward as it may appear. While the TS
term is clearly dependent on the temperature, the entropy value itself (just
S) is also intrinsically dependent on the temperature as well (via the 1/kT
factors in all of the exponentials in the stat mech formulas). Therefore,
just changing the temperature in the MMPBSA.pypp script (line 282) is not
enough. You also need to change the temperature being used in the nmode
function itself (see $AMBERHOME/AmberTools/src/sff/nmode.c and look for
298.15). This is actually the reason we hard-coded the temperature in the
first place, since we didn't want to make changing the temperature seem that
easy (and thus trick people into thinking that gave the right answers).
You'll have to change the temperature in both of these places, then
re-install AmberTools (since nab has to be recompiled in order for the
changed temperature to take effect, and that *new* nab has to be used to
compile the mmpbsa_py_entropy program). This is what is required to change
the temperature each time.
An alternative to this is to just post-process the _MMPBSA_complex_nm.out,
_MMPBSA_receptor_nm.out, and _MMPBSA_ligand_nm.out files yourself and
calculate the entropies from those files. Each of those files *should* have
the vibrational frequencies of each normal mode (just the eigenvalues of the
Hessian), which you can insert directly into the statistical mechanical
formulas for the entropy. Of course you should always check this by
comparing to 298.15 (and the values printed in your output file).
HTH,
Jason
> Best regards,
> Jesper
>
>
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--
Jason M. Swails
Quantum Theory Project,
University of Florida
Ph.D. Candidate
352-392-4032
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Received on Mon May 23 2011 - 10:30:04 PDT
