Hi Chris<br><br>Thank you for your note!<br><br>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?
<br><br>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.
<br><br>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?
<br><br>Thank you again<br><br><div><span class="gmail_quote">On 9/8/06, <b class="gmail_sendername"><a href="mailto:chris.neale@utoronto.ca" target="_blank" onclick="return top.js.OpenExtLink(window,event,this)">chris.neale@utoronto.ca
</a></b> <<a href="mailto:chris.neale@utoronto.ca" target="_blank" onclick="return top.js.OpenExtLink(window,event,this)">chris.neale@utoronto.ca</a>> wrote:
</span><blockquote class="gmail_quote" style="border-left: 1px solid rgb(204, 204, 204); margin: 0pt 0pt 0pt 0.8ex; padding-left: 1ex;">Having actually looked back at my notes, here is what I did to extend pope.pdb<br>into a larger system. However, the suggestion that I posted last time should
<br>work just as well.<br><br>1. Remove all waters<br>2. Duplicate the box until your heart's content. Make it larger than you<br>actually want because the box will collapse to some extent.<br>3. MD with Z-only posre on lipid head groups (X and Y force components = zero).
<br>This step must be done with constant pressure (In this procedure, make sure to<br>use isotropic pressure coupling so that the box max and min z don't come into<br>contact with the membrane).<br><br>NOTE for step 3: It is assumed that your edges line up with each other. Load the
<br>system into vmd and show periodic unit cells to make sure. If they line up<br>poorly then I would find a new starting PDB. However, pope.pdb lines up well.<br><br>4. Adjust the z-dimension to what you want it to be, center your membrane in the
<br>z if you want to.<br>5. solvate the system.<br>6. Remove any waters that were placed within the membrane<br>7. energy minimize<br>8. posre run as before to allow the water to adjust to the membrane surfaces.<br>However, during this run (and all the rest of the steps) I use semiisotropic
<br>Pcoupling.<br>9. equilibration phase without any position restraints<br>10. production run.<br><br>If you are going to add protein, you could do that with the results of step 4<br>since most procedures involve stripping out any waters anyway.
<br><br>Again, the procedure that I outlined previously should work, but I have not<br>tested that procedure, only this one.<br>_______________________________________________<br>gmx-users mailing list <a href="mailto:gmx-users@gromacs.org" target="_blank" onclick="return top.js.OpenExtLink(window,event,this)">
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