Re: [AMBER] RDF vs, Coordination numbers

From: Daniel Roe via AMBER <>
Date: Fri, 22 Jul 2022 10:16:51 -0400


Sorry for the delay in replying to this.

On Thu, Jun 30, 2022 at 12:47 PM Damiano Spadoni via AMBER
<> wrote:
> radial out OutputFileName.dat 0.1 15 :EL_ResidueMask :P_ResidueMask noimage volume center1 center2

I think maybe what you wanted to do here was 'bymol1' or 'byres1' etc.
The 'center1' and 'center2' keywords calculate the RDF from the center
of *everything* in the corresponding mask. So all you are doing here
is binning the distance between the center of mass of everything
selected by :EL_ResidueMask and the center of everything selected by
:P_ResidueMask. Try changing to 'bymol1' and 'bymol2'.

Hope this helps,


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Received on Thu Aug 04 2022 - 13:35:25 PDT
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