Dear All,
I am simulating a membrane bound protein using amber12 and Lipid11 and
ff99SB force fields. The initial 20 residues of the protein goes into the
membrane layer. Therefore, I have taken a pre-equilibrated POPC membrane
layer (256 POPC molecules) which has cylindrical hole of (radius = 12 ang)
in the center. I have manually inserted 1-20 residues of the protein
using VMD and capped rest of the protein with the solvent box. Similarly,
the cholesterol molecules were also manually added. While solvating the
system, VMD has added water molecules around the protein which was inserted
in the membrane. I have few questions about this system:
1.Do I have to remove those water molecules manually before I start the
simulation?
2. What should be minimum distance between the protein residues (inserted
in the membrane layer) and the POPC molecules?
3. Can I remove the water molecules (present between the protein and
membrane) after the system have attained a constant density?
Currently, I am simulating the system with following steps:
1. minimizing with restraining the protein, POPC, cholesterol, and
counterions for 10000 steps
2. minimization for 10000 steps without any restrains
3. Heating (0-100K) with constraining the protein (10 kcal/mol/ang^2) and
lipid (5 kcal/mol/ang^2) for 20ps under NVT
4. Heating (100-300K) under NPT conditions for 100ps with same restrains
5. Equilibrating the system under NPT with npt =2, with similar restrains.
I have equilibrated the system for 5ns. I have verified temperature,
volume, pressure, box dimensions, and density until now
temperature - constant at 300k
volume - is changing
box dimensions - changing
density - varying in between 0.98-0.87
So, I think the system is under the process of equilibration. Any anybody
comment on my three questions?
manikanthan
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Received on Sun Jan 20 2013 - 17:30:03 PST
