[gmx-users] Simulation of membrane protein

Justin A. Lemkul jalemkul at vt.edu
Wed Oct 19 19:37:33 CEST 2011

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 A. Lemkul
Ph.D. Candidate
ICTAS Doctoral Scholar
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu | (540) 231-9080


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