Yes, an empty space is formed in the protein. The protein and lipids
were well packed. Do I have to constrain the bilayer along with the
protein while heating and equilibration (5-10ns) ? If so, no I have
not done that. I am only constraining protein. Thanks for the help.
mani
On Tue, Jan 15, 2013 at 12:25 PM, Benjamin D Madej <bmadej.ucsd.edu> wrote:
> An empty space forms in the protein? Does the protein unfold? This may depend on how you built the structure with VMD. Were the protein and lipids well-packed? There are several ways to prepare a membrane-bound protein system: for example in house packing algorithms, manual positioning with vmd, or the CHARMM-GUI builder. Did you constrain the bilayer as well?
>
> One potential issue is that the volume of the simulation may still be equilibrating in the beginning of production. Have you looked at the temperature, pressure, volume, box dimensions, and density of the simulation in the first nanoseconds? I would take a look at those values.
>
> It may take longer to equilibrate this simulation. For example, a CHARMM-GUI pure bilayer system built with LEaP's default 'setBox' command takes tens of nanoseconds to equilibrate (see the Amber lipid force field tutorial, Lipid11: http://ambermd.org/tutorials/advanced/tutorial16/An_Amber_Lipid_Force_Field_Tutorial.html, http://dx.doi.org/10.1021/jp3059992).
>
> Ben Madej
> Walker Molecular Dynamics Lab
>
> On Jan 15, 2013, at 9:36 AM, manikanthan bhavaraju <mhb75.msstate.edu<mailto:mhb75.msstate.edu>>
> wrote:
>
> Ben,
>
> Thanks for the reply. I am using POPC+cholesterol bilayer system. In
> my case only a part of the protein (1-20 residues) goes into the lipid
> bilayer. So, I have capped rest of the protein with solvent and
> counter ions. I found few articles where the protein was completely
> immersed into the bilayer. I am currently struggling to establish a
> particular simulation procedure for my system. As you have mentioned
> before, initially I have minimized the system for 10,000 steps by
> constraining protein, lipid, and cholesterol molecules. Then, heated
> the system (0-100K) for 10ps under NVT conditions (with protein
> constrained) and then (100-300K) under NPT conditions (with protein
> constrained). Then, under NPT conditions the system was equilibrated
> without any constraints.
>
> But after 1-2 ns of simulations, I have observed a large void in the
> protein. Is there any alternative procedures? Please let me know
> about it.
>
> mani
>
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--
Manikanthan Bhavaraju
Graduate Teaching Assistant
Dept. of Chemistry
Mississippi State University
office no : 662-325-4633
MS -39762
USA.
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Received on Tue Jan 15 2013 - 11:00:03 PST
