[gmx-users] Simulation of membrane protein

James Starlight jmsstarlight at gmail.com
Wed Oct 19 18:16:14 CEST 2011


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.

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 ).

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 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?


> -Justin
> --
> ==============================**==========
> Justin A. Lemkul
> Ph.D. Candidate
> ICTAS Doctoral Scholar
> Department of Biochemistry
> Virginia Tech
> Blacksburg, VA
> jalemkul[at]vt.edu | (540) 231-9080
> http://www.bevanlab.biochem.**vt.edu/Pages/Personal/justin<http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin>
> ==============================**==========
> --
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