AMBER Archive (2006)

Subject: Re: AMBER: Calculation of g(r) from PTRAJ

From: David A. Case (
Date: Mon Apr 17 2006 - 11:45:27 CDT

On Sun, Apr 16, 2006, Ananda Rama Krishnan Selvaraj wrote:

> I have made the MD simulation for organic system at
> different temperatures without using any solvents. Now, i am interested
> to calculate the radial distribution function <g(r)> from PTRAJ of
> AMBER7 version.
> In the manual, the syntax for the calculation of g(r)function is given
> for solvent and solute system.

The terms "solvent" and "solute" are somewhat arbitrary. The radial command
should compute distribution functions atoms in the "solute-mask" and those
in the "solvent-mask". It doesn't real know anything about whether the atoms
you choose are "really" (physically) solvent or not.

...hope this helps...dac

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