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

From: Daniel Roe <>
Date: Mon, 1 Jul 2013 10:30:56 -0600


On Mon, Jul 1, 2013 at 3:51 AM, kurisaki
<> wrote:
> Then, I would like to know how to ignore such intramolecular bonds
> when I calculate RDF of water by using ptraj command, "radial".

Unfortunately there is currently no option to do this in ptraj or
cpptraj. However, this option may be enabled in a future update of

> I use AmberTools12 here.

It may be worthwhile for you to update to AmberTools13, which includes
many bug fixes and enhancements to the code overall. One feature that
may interest you (if you have access to a multi-core machine) is that
the 'radial' action is one of several actions that have been
OpenMP-parallelized in cpptraj.


Daniel R. Roe, PhD
Department of Medicinal Chemistry
University of Utah
30 South 2000 East, Room 201
Salt Lake City, UT 84112-5820
(801) 587-9652
(801) 585-9119 (Fax)
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Received on Mon Jul 01 2013 - 10:00:03 PDT
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