1) If you don't think the protein is solvated inside the membrane (which
seems pretty unlikely) you should remove them. For the water to leave the
membrane through minimization or MD may take an extremely long time.
2) You should be able to estimate that distance from known crystal
structures of membrane proteins that were solved with detergent molecules
present. I would guess something along the order to ~2 Angstroms
3) If you do this, you'll have to re-equilibrate after.
In general you should estimate the equilibration of the system in two ways:
A) the RMSD of the protein (it should become constant)
B) the potential energy of the system. Since you are running at constant
temperature, the energy may change over time (it is not a constant energy
simulation), but nevertheless you expect the potential energy to settle out
to some extent as it reaches a more natural configuration. You could also
consider looking at the pressure, and expect to see it equilibrate.
What do you mean by "restraints" on the protein and the membrane? I don't
see why the membrane or counterions should be restrained at all, and the
protein should potentially only be restrained initially to a particular
position in the membrane or to within a certain RMSD to ensure it doesn't
unfold if the initial placement is very bad.
There are tools online that allow you to for instance make a membrane
bilayer of a particular composition and insert a protein into it. That is,
they will automatically calculate which membrane lipids should be removed
to fit the protein without overdoing it. This might allow for faster
equilibration than the big cylindrical hole you are now making, but perhaps
its not worth it.
~Aron
On Sun, Jan 20, 2013 at 7:59 PM, Manikanthan Bhavaraju <
manikanthanbhavaraju.gmail.com> wrote:
> 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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>
--
Aron Broom M.Sc
PhD Student
Department of Chemistry
University of Waterloo
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Received on Sun Jan 20 2013 - 19:00:03 PST
