[gmx-users] gmx freevolume

[Federico Gallino]

Dear All,

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.

E.g:

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=1-density*Vw/MW

I got:

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.

Best regards,

Federico


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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