[gmx-users] Simulation of membrane protein

[James Starlight]

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

>
>
>>
>   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?



James
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