[AMBER] Anomalous peak of RDF of water when using ptraj of AmberTools12

From: kurisaki <kurisaki.ncube.human.nagoya-u.ac.jp>
Date: Mon, 1 Jul 2013 18:51:20 +0900

Dear Amber users and developers

I'm now trying to calculate RDF in terms Wat,
preparing the ptraj input as shown below.

trajin protein-wat.mdcrd
radial RDF_H-vs-O 0.1 75 :WAT

However, I found an anomalous peak around 1[A],
This would be due to intra-molecular bonds betwenn H and O of water molecules.

Then, I would like to know how to ignore such intramolecular bonds
when I calculate RDF of water by using ptraj command, "radial".

Yours sincerely,

                                                Ikuo KURISAKI

I use AmberTools12 here.

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Received on Mon Jul 01 2013 - 03:00:02 PDT
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