Dear Professor Roe,
Thank you for your advices,
I'll try AT13.
Yours sincerely,
IK
-----Original Message-----
From: Daniel Roe [mailto:daniel.r.roe.gmail.com]
Sent: Tuesday, July 02, 2013 1:31 AM
To: AMBER Mailing List
Subject: Re: [AMBER] Anomalous peak of RDF of water when using ptraj of
AmberTools12
Hi,
On Mon, Jul 1, 2013 at 3:51 AM, kurisaki <kurisaki.ncube.human.nagoya-u.ac.jp>
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 cpptraj.
> 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.
-Dan
--
-------------------------
Daniel R. Roe, PhD
Department of Medicinal Chemistry
University of Utah
30 South 2000 East, Room 201
Salt Lake City, UT 84112-5820
http://home.chpc.utah.edu/~cheatham/
(801) 587-9652
(801) 585-9119 (Fax)
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Received on Mon Jul 01 2013 - 18:30:03 PDT
