[gmx-users] perfluorohexane pdb... again

[Ángel Piñeiro]

Hi Marcelo
your molecules are not in a box, the head of the pdb you sent to me is:

HEADER 
TITLE     Built with
Packmol                                             
REMARK   Packmol generated pdb file 
REMARK   Home-Page: http://www.ime.unicamp.br/~martinez/packmol
REMARK
ATOM      1  C1  HEX A   1      17.953  31.169   8.840  1.00 20.00
C+0
ATOM      2  C2  HEX A   1      18.510  32.451   9.461  1.00 20.00
C+0
ATOM      3  C3  HEX A   1      18.321  33.614   8.486  1.00 20.00
C+0
ATOM      4  C4  HEX A   1      18.878  34.896   9.108  1.00 20.00
C+0
ATOM      5  C5  HEX A   1      18.689  36.059   8.133  1.00 20.00
C+0


there are no walls there.

Cheers,

Ángel.



On Tue, 2011-01-11 at 20:31 +0000, Marcelo Silva wrote:

> Angél,
> 
> I'm sending you my initial pdb in attachment. I chose the box size to 
> fit the experimental density.
> I am just trying to get simple properties of the pure compounds hexane 
> and perfluorohexane and of a mixture 0.5 hexane/perfluorohexane (density 
> mainly). But maybe I just need a long molecular dynamics equilibation 
> step rather than simulated annealing to get a good starting configuration.
> Perhaps what went "wrong" is that the system was at temperatures much 
> higher than hexane boiling point and it started to form clusters.
> 
> Best regards,
> 
> Marcelo


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