[gmx-users] Simulation of membrane protein

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

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 
less likely to help you.

> 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 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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