Anirban Ghosh skrev 2011-05-19 11.58:
Hi ALL,
I am trying to calculate the lateral diffusion coefficient of a
protein in a bilayer (CG simulation using MARTINI FF). The simulation
length is 5 micro-seconds. I wanted to know based on what should i set
the values of -beginfit and -endfit and also the value for -trestart.
Is it necessary to set -trestart?
Thanks a lot in advance.
Regards,
Anirban
-trestart is in principle not necessary, but will provide better
statistics. It will also increase the calculation time. -beginfit and
-endfit should be set to exclude non-linear (non-converged) part of the
msd plot.
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Erik Marklund, PhD student
Dept. of Cell and Molecular Biology, Uppsala University.
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er...@xray.bmc.uu.se http://folding.bmc.uu.se/
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