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, [EMAIL PROTECTED]
<[EMAIL PROTECTED]> 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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