[AMBER] cpptraj rotdif parameters

From: Alegrete, Matthew <matthew.alegrete.28.my.csun.edu>
Date: Thu, 10 Jul 2014 12:34:29 -0700

I am currently trying to analyze the rotational diffusion in a few
simulations, but am having trouble understanding some of the parameters
that go into the cpptraj script for the rotdif action. I have already
consulted the documentation as well as other emails in the reflector and
haven't found anything.

In the example given in the manual, "nvecs" was given equal to the number
of frames. Is that generally the way this number should be picked? Was
there any significance in the example of picking "ncorr" to be 90% of the

Are the times "ti" and "tf" arbitrarily picked limits for integrating the
correlation function, or should they be the times you want to sample the
trajectory between? Also, should the "dt" match the time step used in the
simulation, or is that again an arbitrary integration step?

I am suspicious that short trajectories may cause problems with
convergence. Increasing the number of iterations (itmax) seems to help the
small anisotropic analysis converge, but the amoeba minimizer is where
convergence keeps failing.

Any insight as to the best way to find optimal values for these parameters
(nvecs, ncorr, ti, tf, dt, itmax) would be greatly appreciated. So far I
have just been experimenting but numbers that converge on one trajectory
fail on trajectories for systems that are identical in every way but the
temperature they are equilibrated at.

Thank you,
Matt Alegrete
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Received on Thu Jul 10 2014 - 13:00:02 PDT
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