[gmx-users] gmx freevolume
Federico_Gallino at saes-group.com
Mon May 29 15:42:26 CEST 2017
I would like to put your attention on the output of gmx freevolume.
I cannot understand how the "Molecular van der Waals volume" is computed.
I made some crosschecks from the FFV but I never got the value written by gmx.
Free volume 35.97 +/- 0.00 %
Total volume 68.07 +/- 0.00 nm^3
Number of molecules 64 total mass 51773.89 Dalton
Average molar mass: 808.97 Dalton
Density rho: 1263.06 +/- 0.00 nm^3
Molecular volume Vm assuming homogeneity: 1.0635 +/- 0.0000 nm^3
Molecular van der Waals volume assuming homogeneity: 0.6810 +/- 0.0000 nm^3
Fractional free volume 0.168 +/- 0.000
If I use the empirical correlation formula:
FFV=-0.06326 vs FFv=0.168 (gmx freevolume, see above)
Vice versa if I compute Vw I got:
Vw= 0.748086 vs Vw=0.6810 (gmx freevolume, see above)
In the manual, it is written that the algorithm come from the paper from Bondi, that is similar to the ones from Van Krevelen.
I applied the Van Krevelen group contribution approach and I got:
Vw=0.728 in good agreement with the formula above but in disagreement with the output from gmx freevolume
Thank you in advance for any clarifications.
Federico Gallino, Ph.D.
Computational Science & Engineering
mail: federico_gallino at saes-group.com
T: +39 02 93178316
Fax: +39 02 93178460
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