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AMBER Archive (2003)Subject: diffusion in ptraj
From: Ioana Cozmuta (ioana_at_nas.nasa.gov)
Hi,
I have a question about the message posted in ptraj when doing a diffusion
To calculated diffusion constants, calculate the slope of the
This is not clear to me. As far as I know diffusion constants, D, are
if log log plotted the eq above becomes
meaning that one should do a fit with two parameters: the ofset A0 and the
D = exp(A0)/6 in units of A^2/ps
As far as I can see from the code the data dumped in the output files are
Why is the preference towards a regular plot instead of log-log plot?
I would appreciate your comments.
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