[AMBER] Raw RDF exceeds total number of waters?

From: Matthew Guberman-Pfeffer via AMBER <amber.ambermd.org>
Date: Thu, 8 Sep 2022 14:54:44 -0400

Dear Amber Community,

The below CPPTRAJ command gives me raw RDF values that exceed the number of waters in the simulation box:

 radial out rdf.dat 0.1 15 :WAT,Na+ :1280 density 0.033456 intrdf intrdf.dat rawrdf rawrdf.dat bymol1

Is it an imaging issue?

What I’m really concerned about is the same command run on two different trajectories with identical counts of WAT and Na+ gives me raw RDF values that almost systematically differ by a factor of ~2. The only difference between the simulations is the temperature. I need to know if the difference is real.


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Received on Thu Sep 08 2022 - 12:00:02 PDT
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