Referring to subject, I had no answer to my question if solvate box (added
21847 residues, density 0.792) is preferable to solvateoct (added 30286
residues, density 0.867). Therefore, I assume this means carrying out MD with
solvatebox.
My question now is how to carry out equilibration for this system. The pore
protein entails a docked large ligand (118 atoms) within the pore, coming from
amber rescore in DOCK. It was immersed in a POPC membrane, where the polar
heads of POPC are solvated TIP3P. Then the whole was TIP3PBOX solvated with
12.0 A buffer.
Summing up all that I could learn from the literature,I guess that the system
should be first energy minimized with protein-complex restrain (SHAKE on H
atoms and PME). For membrane I found indications of ca. 30 kcal/molxA^2. No
idea how that could be applied to my protein-complex.
Once that (or a more reasonable) pre-equilibration is carried out, I suppose to
have to gradually "heat" the system to 300K at constant volume. Here surely the
protein complex should be restrained as above. However, probably the POPC
molecules should also be restrained (or only their polar head?).
With this second step (or a more reasonable one) the system should be ready for
pre-MD at 300K and 1 atm, initially with the above restrain on the protein
complex (and probably the lipid). Gradually (after how many ps?) restraint on
the protein (and lipid, if any was applied) should be removed.
Now the system should be ready for production MD, under SHAKE for H atoms.
In view of the computational burden, I would appreciate any guidance.
Thanks
francesco pietra
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Received on Sun Dec 02 2007 - 06:07:06 PST
