# [gmx-users] Simulation of membrane protein

Justin A. Lemkul jalemkul at vt.edu
Mon Oct 17 22:22:07 CEST 2011

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James Starlight wrote:
> Justin
>
>
>
>     I can't access the file, so I don't know.  20 iterations still
>     doesn't sound like enough for the tutorial system, unless you shrunk
>     faster than what was recommended.
>
>
> 20 iteration was a simple example. It means that many iterations
> produced more accuracy results in comparison to previous one :)

OK, please be literal in the future.  Providing incorrect or inaccurate
information slows you down on your goal to getting a resolution and makes people

> Its only one not understood for me.
> After 20 iterations I've obtained S per lipid value= 0.2 nm^2. It's
> equal to 2 A^2 ( 1A=0.1 nm) http://en.wikipedia.org/wiki/Angstrom

I am familiar with this unit conversion.  0.2 nm^2 is, however, 20 A^2 (mind the
square term).

> Why you told in the tutorial that experimental value was 65 A^2 ?
>

Because it is.  Different techniques give slightly different results, but
generally 0.62 - 0.65 nm^2 is an accepted value for the APL of DPPC.

If you have achieved 0.2 nm^2, you have greatly overcompressed your box.  Either
you did far more shrinking steps than is called for, or you scaled down much too
quickly.  The procedure of 26 shrinks with a 0.95 scaling factor produces a very
reproducible result.  You should stick to it.

>
>
>
>       Perhaps the value you have set in vdwradii.dat for C radii is too
>     large for genbox to function properly.
>
>
> It seems that this is true because I've defined vdv radii as 0.4 instead
> of 0.375. Could the differense in the 0.015 result in the error?
>
>

Likely the error comes from the fact that your box is extremely small, but I
would also advise you to not make ad hoc changes to the values shown in the
tutorial.  They are there for a reason.  I have found that a 0.4 nm carbon
radius gives undesirable result (an overall lack of sufficient hydration).

Check your box dimensions in the last shrunken .gro file you produced.  If the
x/y dimensions are any less than 6 nm or so, you've gone too far.  In fact, you
should be aiming to reproduce whatever the box dimensions were of the original
DPPC membrane.

-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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