On 2011-03-27 07.36, Elisabeth wrote:
Dear all,
I am trying to calculate Cv of a pure alkane 125 molecules with actual
density, and here is what I have done:
As indicated in an earlier post this is a non-solved problem, but we are
working on it.
The computation of heat capacity in g_energy was erroneous and it has
been removed in 4.5.4. A better version will be implemented soon, but
removing it was better than giving the wrong result.
For now you want to compute the variance in the enthalpy and divide
those by kB T^2 (for NPT simulations) respectively the variance in the
total energy (for NVT simulations).
You then need to correct for harmonic degrees of freedom (see manual
chapter 1). And then do quantum corrections by doing a normal mode
analysis... As said we have a paper about this coming up.
1-
Cv: Run NVT > g_energy>select T and Etot=total energy
As I issue g_energy *.edr
Heat Capacity Cv:12.4787 J/mol K (factor = 0.000369503)
And when I choose –nmol XXX
Heat Capacity Cv:13.4007 J/mol K (factor = 0.0462137)
- Do I have to use –nmol? What would be the unit with –nmol ?
and as I issue g_energy using 4.5.3
Temperature dependent fluctuation properties at T = 299.987. #constr/mol = 0
Heat capacity at constant volume Cv: 341.734 J/mol K
and with -nconstr # of bonds
Temperature dependent fluctuation properties at T = 299.987. #constr/mol
= 19
Heat capacity at constant volume Cv: 262.746 J/mol K
- From this I am guessing what 4.0.7 reports is not correct!?
but still what I am getting from 4.5.3 is far from actual reported value
(around 170). I guess I am missing something..! or Is the difference
acceptable?
g_energy says:
you will need to give the number of constraints per molecule –nconstr
- so I need to count how many bonds are fixed in the molecule as I am
setting constraints= all-bonds?
The way to this is counting no. of bonds? What about macromolecules? Is
there an easier way of finding number of constraints?
2-
Cp:
I did NPT, g_energy *.edr -nmol XXX -nconstr (4.5.3)
I want to select T and enthalpy but since enthalpy is not on the list I
select total-energy (which is Etot I think) and pv terms but g_energy is
still giving Cv!
Property Energy terms needed
---------------------------------------------------
Heat capacity Cp (NPT sims): Enthalpy, Temp
Energy Average Err.Est. RMSD Tot-Drift
-------------------------------------------------------------------------------
Total Energy 86.1571 0.085 1.55565 -0.0944531
(kJ/mol)
Temperature 300.074 0.07 5.77219 0.318146
(kJ/mol)
pV 15.8128 0.061 1080.82 -0.249203
(kJ/mol)
Temperature dependent fluctuation properties at T = 300.074. #constr/mol
= 19
Heat capacity at constant volume Cv: 325.067 J/mol K
Can you please guide me where the problem lies?
-------------------------------------------------------
again Cv : to compare with constraints=none
but still -nconstr should be on otherwise I values are more off.
Total Energy 132.418 0.051 1.77314 0.144794
(kJ/mol)
Temperature 300.008 0.052 4.50209 0.15866
(kJ/mol)
Temperature dependent fluctuation properties at T = 300.008. #constr/mol
= 20
Heat capacity at constant volume Cv: 442.016 J/mol K
3-
Thermal expansion coeff. (NPT): Enthalpy, Vol, Temp
Isothermal compressibility: Vol, Temp
Adiabatic bulk modulus: Vol, Temp
Since volume appears for calculation of the above properties , does this
imply only NPT results in these properties?
and wanted to make sure what 4.5.3 reports is reliable..
Many thanks for you time!
Best,
--
David van der Spoel, Ph.D., Professor of Biology
Dept. of Cell & Molec. Biol., Uppsala University.
Box 596, 75124 Uppsala, Sweden. Phone: +46184714205.
[email protected] http://folding.bmc.uu.se
--
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