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

chris.neale at utoronto.ca chris.neale at utoronto.ca
Fri Sep 8 03:46:01 CEST 2006

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 
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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