James Starlight wrote:
Justin,
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.
Ok.
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
hydrated membrane.
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
--
========================================
Justin A. Lemkul
Ph.D. Candidate
ICTAS Doctoral Scholar
MILES-IGERT Trainee
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu | (540) 231-9080
http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin
========================================
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