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
--
========================================
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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