[gmx-users] perfluorohexane pdb... again

Ángel Piñeiro angel.pineiro at usc.es
Tue Jan 11 19:24:44 CET 2011

Hi Marcelo
It is always good to see what happens to a known molecule before working
with your target with a new methodology. I took a closer look to your
pdb. You do have different hexane conformations. Anyway it is hard to
believe that your initial box was full of hexane... could you check
again your initial pdb file? could you paste the head of the initial pdb
file to see the box dimensions? The final pdb file is a cubic box of
4.72 nm each edge. I do knot know what are you looking for with your
system but why don't you run a longer MD simulation at 298 K at constant
pressure to get the right density of the system? you should get a
variety of different reliable conformations with different probability
that you could group in clusters if you are interested in that.



On Tue, 2011-01-11 at 17:44 +0000, Marcelo Silva wrote:

> Hello Angél,
> I started with hexane just to know what would happen and then I would
> apply the same procedure to perfluorohexane.
> I used a NPT box with 500 hexane molecules using packmol. The system
> was initially homogeneous.
> Then I ran energy minimization with steepest descent (em.mdp) and the
> simmulated annealing afterwards with no constraints (sa.mdp). It's the
> first time I am using SA as I think this would be a good way of having
> a good starting box. I used the OPLS-AA force field.
> The mdp's are in the attachment. 
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