[gmx-users] perfluorohexane pdb... again

Marcelo Silva jokler79 at hotmail.com
Tue Jan 11 18:49:24 CET 2011

I'm sorry to send another message but the sa.mdp file I sent was an old one

Best regards

From: jokler79 at hotmail.com
To: gmx-users at gromacs.org
Subject: RE: [gmx-users] perfluorohexane pdb... again
Date: Tue, 11 Jan 2011 17:44:50 +0000

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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