[gmx-users] Simulation of membrane protein
Justin A. Lemkul
jalemkul at vt.edu
Wed Oct 19 19:37:33 CEST 2011
James Starlight wrote:
> I don't need the files. I'm just trying to save you time. If I
> want to see a coordinate file, I'll ask for it to be sent to me
> directly. I have seen no such need yet.
> Application of pressure causes the box to change. The water won't
> leak in during NVT because the components of the system are trying
> to keep the box full since its dimensions are invariant. Such
> leakage is typical during equilibration, as I've said. You should
> not be alarmed by this result.
> So presence of several water molecules within the membrane after
> equilibration will not cause futher errors in simulation, won't it?
> After 1 ns MD simulation of my system I've found that some waters were
> excluded from the bi-layer.
It won't cause errors, per se, but it does indicate that your system is not
equilibrated (nor should you expect it to be after only 1 ns). After 20 ns or
so of equilibration, most membrane systems should be devoid of internal water
and should be well-equilibrated.
> By the way the system prepared by G_membed consisted of more water
> molecules within the membrane after solvation via Genbox ( I've used vdv
> radius of 0.5 for carbons ).
0.5 is definitely overkill; I've never obtained good results with any value
greater than 0.375. Usually you'll have insufficient water to have a fully
> Finally, I'd like to analyse results obtained after 1ns simulation.
> Firstly I want to compare some physical values of my system with the
> experiment. I found that I can analyse some such parametries like A per
You'll never get a good comparison.
> lipid ( I've already known this experimental value) as well as *Density
> of the Membrane and the coefficent of the **Lateral Diffusion for
> Lipids. Where I could found last two experimental values for my system
> as well for other lipids?
Search the literature.
Justin A. Lemkul
ICTAS Doctoral Scholar
Department of Biochemistry
jalemkul[at]vt.edu | (540) 231-9080
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