[AMBER] rdf

From: subrata paul <paul.subrata34.gmail.com>
Date: Wed, 5 Jan 2011 17:18:31 +0400

Dear amber user

I am simulating a water box in amber10.Which has only SPC water.
Now i want to calculate Ow-Ow rdf and Ow-Hw rdf . My ptraj input is

*trajin xxxx.mdcrd
radial Ow_Oh_rdf .01 10 :WAT.O :WAT.H

when i calculate rdf for this input no hydrogen atom is detecting.
But When I write :WAT.H1,it detecting the H1 atom .
Which gave a RDF plot. But is not giving a good plot.

is there my input is wrong ?? or is my atom selection wrong.

please help me regarding this.

thanking You
AMBER mailing list
Received on Wed Jan 05 2011 - 05:30:06 PST
Custom Search