[gmx-users] Re: Simulation problem with extended membrane system!

liu xin zgxjlx at gmail.com
Fri Sep 8 10:35:25 CEST 2006

Hi Chris

Thank you for your note!

According to your suggestion, I did a energy minimization and then a MDS
with "freezegrps=SOL, freezedim=N, N, Y", the rest of the system were
simulated with no constraint. This time I use semiisotropic pressure
coupling with tau_p=5. The system will be equilibrated with water
constrained for 1ns, do you think it's enough?

The reason why I want to extend the system is because that I've got a GPCR,
and I want to simulate it in a DPPC membrane environment, but the z
dimension of the membrane, downloaded from Dr. Tielman's websit,  was not
large enough, when I align the protein to the z axis of the membrane I find
the two ends of the protein are poking out of both water layers.

Back to the previous question, after solvate the lipids in water, can I
remove the water placed in the membrane with excel instead of script? Cause
with editconf we can know the z dimension of the lipids_only system, let's
say 6, so if I center the whole system with 0 0 0, the water molecules with
z coordinates below 3 and above -3 will be excluded. If I'm right, I think
excel can do it too, or the scripts have some advantages?

Thank you again

On 9/8/06, chris.neale at utoronto.ca <chris.neale at utoronto.ca> wrote:
> 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 =
> zero).
> 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
> well.
> 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
> surfaces.
> However, during this run (and all the rest of the steps) I use
> semiisotropic
> Pcoupling.
> 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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