[gmx-users] gmx freevolume

[Mark Abraham]

Hi,

I have no idea, but David van der Spoel implemented this tool, so perhaps
forward your gmx-users query to him personally?

Mark

On Mon, May 29, 2017 at 3:43 PM Federico Gallino <
Federico_Gallino at saes-group.com> wrote:

> 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 <+39%2002%209317%208316>
> Fax: +39 02 93178460 <+39%2002%209317%208460>
>
> [cid:0__=4EBB0AAEDFA32D278f9e8a93d at saes-group.com]
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