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JMiranda jmiranda at explicacoes.com
Mon Sep 11 23:56:46 CEST 2006

gmx-users-request at gromacs.org 

-----Original Message-----
From: gmx-users-bounces at gromacs.org [mailto:gmx-users-bounces at gromacs.org]
On Behalf Of chris.neale at utoronto.ca
Sent: sexta-feira, 8 de Setembro de 2006 2:46
To: gmx-users at gromacs.org
Subject: [gmx-users] Re: Simulation problem with extended membrane system!

Having actually looked back at my notes, here is what I did to extend
pope.pdb into a larger system. However, the suggestion that I posted last
time should work just as well.

1. Remove all waters
2. Duplicate the box until your heart's content. Make it larger than you
actually want because the box will collapse to some extent.
3. MD with Z-only posre on lipid head groups (X and Y force components =
This step must be done with constant pressure (In this procedure, make sure
to use isotropic pressure coupling so that the box max and min z don't come
into contact with the membrane).

NOTE for step 3: It is assumed that your edges line up with each other. Load
the system into vmd and show periodic unit cells to make sure. If they line
up poorly then I would find a new starting PDB. However, pope.pdb lines up

4. Adjust the z-dimension to what you want it to be, center your membrane in
the z if you want to.
5. solvate the system.
6. Remove any waters that were placed within the membrane 7. energy minimize
8. posre run as before to allow the water to adjust to the membrane
However, during this run (and all the rest of the steps) I use semiisotropic
9. equilibration phase without any position restraints 10. production run.

If you are going to add protein, you could do that with the results of step
4 since most procedures involve stripping out any waters anyway.

Again, the procedure that I outlined previously should work, but I have not
tested that procedure, only this one.
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