I wish to know if we should keep some features of production runs of membrane-protein simulations such as useFlexibleCell or useConstantArea or wrapAll for SMD or ABF simulations, or we just use the outcome of these simulations as an equilibrated system. Thank you in advance.
I don't know details of you system, but I assume that you want to simulate transport through the membrane. Based on this assumption I suggest the following:
useFlexibleCell is a good idea in case of anisotropic system such as membrane, especially if you want to apply an artificial force by SMD or ABF. The pressure dispersion will be different in the plane of the membrane and in the solvent - leave it on.
I would turn useConstantArea off. This option turned on would keep the area of your membrane constant during the simulation, which is not what you want in studying transport through membranes. Channels undergo conformational changes in the process, affecting the surrounding membrane. Not allowing the membrane to expand in such case doesn't seem to resemble any "real" biological phenomenon.
wrapAll will not hurt the simulation. Just make sure that you use proper force and your membrane is big enough, so it will not roll over periodic images... :) If the protein of interest is placed in the middle of the membrane, you will not have problems in analysis of the results of your simulations.
Good Luck
Dear Grzegorz,
Thank you so much for your worthwhile suggestions and complete explanations. Undoubtedly, they were very, very helpful to me.
Regards
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