Dear Mr.David,
Thank you
anand
----- Original Message -----
From: "David A. Case" <case.scripps.edu>
Date: Monday, April 17, 2006 6:45 pm
Subject: Re: AMBER: Calculation of g(r) from PTRAJ
> 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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Received on Tue Apr 18 2006 - 03:02:42 PDT
