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

-----------------------------------------------------------------------
The AMBER Mail Reflector
To post, send mail to amber_at_scripps.edu
To unsubscribe, send "unsubscribe amber" to majordomo_at_scripps.edu