Am 04.03.2009 um 17:32 schrieb Michael Lerner:
Hey Michael
You probably know all of this, but I thought I'd mention it in case
someone was tempted to just take your code and apply it individually
to each frame of a simulation without really thinking about it.
Unfortunately, I've seen people make this particular error a few
times (in both VMD and C), and usually you can't tell they're making
it just by reading their Methods section :(.
Yes you're absolutely right about this, you should never do this
without at least visually checking if this is correct.
The main usage for me is that I don't wanna create complex index files
for gromacs with gromacs' make_ndx tool but instead check the index
groups before or create them from pymol. I used this on the first
frame only - so faar to check diffusion in leaflets separately. What
one can try to do - if you need it every step and the bilayer bends to
much - is to make the whole selection and determination of middle
point locally, only with lipids in a certain range around the specific
one.
But this is then probably a couple more lines :-)
Best
Martin
