[gmx-users] Simulation of membrane protein
Justin A. Lemkul
jalemkul at vt.edu
Mon Oct 17 22:22:07 CEST 2011
James Starlight wrote:
> 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
> 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
Justin A. Lemkul
ICTAS Doctoral Scholar
Department of Biochemistry
jalemkul[at]vt.edu | (540) 231-9080
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