Myunggi Yi wrote:
Thank you all of you.
I've got a pre-equilibrated hydrated POPC bilayer from a web-site.
I made a hole, and I placed my protein.
Now, what is the next step?
If you're asking this, then you'll want to read most of the links from
this site http://wiki.gromacs.org/index.php/Beginners, particularly the
one listed under "S" :-)
Note also, that having a "pre-equilibrated" system in a .pdb file is not
worth anything much. These don't come with velocities, and so you'd need
to equilibrate them once you generate them. If you changed the box size
and added more or less solvent, you'll need to equilibrate that. If
you're worried about distorting the system during the equilibration,
that's what position restraints are for. See man pdb2gmx, and chapters 4
and 5 of the GROMACS manual.
Mark
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