Re: [AMBER] rdf

From: Thomas Cheatham III <>
Date: Wed, 5 Jan 2011 14:57:45 -0700 (Mountain Standard Time)

> 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
> *input
> *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.

You likely do not need to go down to 0.01 angstrom bin sizes; 0.1 angstrom
is sufficient. To select all the hydrogens, :WAT.H*

"Not giving a good plot" is not descriptive enough. Typically, radial
distribution functions around a single group (or water) are more noisy
than over the bulk. Check the ptraj output to see if the appropriate
residues are being selected.

Note however that I just calculated some radial distributions
for water from 500 snapshots (500 ps) and the results seem fine. In fact,
I see little difference between O - H* and O - H1.

Other things to check. "image" the trajectory. Then turn off imaging in
radial to speed up the calculation considerably...

 trajin xxxx.mdcrd
 image familiar
 radial Ow_Oh_rdf .1 15.0 :WAT.O :WAT.H* noimage
 radial Ow_Ow_rdf .1 15.0 :WAT.O noimage


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Received on Wed Jan 05 2011 - 14:00:02 PST
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