[gmx-users] Help with water decane interface

Ángel Piñeiro fangel at usc.es
Sun Mar 30 16:00:02 CEST 2008

This reference  J. Phys. Chem. B , 112 (2008), 3529 could be helpful.


Angel Piñeiro.



De: gmx-users-bounces at gromacs.org [mailto:gmx-users-bounces at gromacs.org] En
nombre de fabracht sdf
Enviado el: domingo, 30 de marzo de 2008 06:49 a.m.
Para: gmx-users at gromacs.org
Asunto: [gmx-users] Help with water decane interface


Dear Gromacs users. I ve been trying to run a MSD for a G coupled receptor
and encountered some problems during my run. 
I have encountered a methodology that deals with this type of transmembrane
proteins, and apparently I need to assemble my box with a "tri" layer,
water/decane/water. I found an article entitled "A molecular Dynamics Study
of the Decane/water interface", where the author studies several aspects in
the usage of such boxes.
I need help on how to put together all these water molecules and decane
molecules in the same box. 
I thought about simply creating theses boxes in separate using gromacs, and
then simply copying and pasting the coordenates of the molecules into the
same topology file. Apparently I was too naive to think that this simplistic
approach would actually work.
Thank you in advance 

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