[gmx-users] perfluorohexane pdb... again

Ángel Piñeiro angel.pineiro at usc.es
Tue Jan 11 23:06:17 CET 2011

Hi Marcelo
your initial box is right, (4.72 nm)^3 = 105.15404e-27 m^3
500 hexane molecules = 500/(6.02e23)*86.16e-3 kg
the density of your initial system = 680.200377454 kg m^-3

The pdb file you sent contained two different structures (I just
realized about this) the first one is in a box of the right dimensions
but the second one, I guess the final frame, is in a much larger box
(8.1315 nm each edge). Your SA at 1000 K and at constant pressure
expands the system a lot and you are not simulating long enough at 298 K
to go back to the right density, that's all.



On Tue, 2011-01-11 at 21:27 +0000, Marcelo Silva wrote:

> Hi Angél,
> Packmol doesn't add the box dimensions in the pdb, but I've created a
> cube with side 4.72 nm in the input file.

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