AMBER Archive (2006)

Subject: Re: AMBER: Ptraj: radial distribution and correlation coefficient

From: Thomas Cheatham (tec3_at_utah.edu)
Date: Tue Nov 14 2006 - 12:34:57 CST


> I am using ptraj to calculate some radial pair distributions between
>
> It seems the second column represents rpd values. Would be glad to know
> what the third column stands for?

The integrated value (occupancy).

> I am also calculating correlation coefficients from the same trajectory.
> Here is my input file:
>
> trajin md.crd
> vector vec :1-3 dipole
> analyze correlationcoefficient {vec | ALL}

That syntax means specify a vector name or ALL, so

analyze correlationcoefficient ALL

or

analyze correlationcoefficient vec

--tec3_at_utah.edu

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