> 4) Am I doing all of this completely backwards from the get go? I am
> following the principles outline here (
> http://link.springer.com/article/10.1023%2FA%3A1011241030461) which use
> correlation functions, but it seems like the cpptraj functions rotdif can
> potentially yield the same information. Do you have any recommendations on
> which method I should proceed with?
In the end, to obtain spectral densities you need to compute a time
correlation function for each H-H vector. These correlation functions
are usually approximated by a product between a rigid body and an
internal part. Rotdif will help with getting information on the
rigid-body rotation of your molecule (ie the full diffusion tensor).
Rotdif should be a good choice since it does not approximate the rigid
body motion as isotropic (as it is done in the paper mentioned above).
George Giambasu
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Received on Thu Oct 30 2014 - 11:30:02 PDT
