[EMAIL PROTECTED] -----Original Message----- From: [EMAIL PROTECTED] [mailto:[EMAIL PROTECTED] On Behalf Of [EMAIL PROTECTED] Sent: sexta-feira, 8 de Setembro de 2006 2:46 To: gmx-users@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 = 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. _______________________________________________ gmx-users mailing list gmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users Please don't post (un)subscribe requests to the list. Use the www interface or send it to [EMAIL PROTECTED] Can't post? Read http://www.gromacs.org/mailing_lists/users.php _______________________________________________ gmx-users mailing list gmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users Please don't post (un)subscribe requests to the list. Use the www interface or send it to [EMAIL PROTECTED] Can't post? Read http://www.gromacs.org/mailing_lists/users.php
