[gmx-users] Simulation of membrane protein

James Starlight jmsstarlight at gmail.com
Mon Oct 17 21:46:10 CEST 2011


> 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?

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