[AMBER] help in radial command

From: Robin Jain <robinjain.chem.gmail.com>
Date: Fri, 26 Jun 2015 10:50:22 +0530

Dear Users,
The value of the integration is around 1000-5000 while i have only 128
solvent molecule, for test run i used spacing 0.002 but got again poor
integration , what is going to be wrong. Is their density problem or other

Message: 34
Date: Thu, 25 Jun 2015 08:46:12 -0600
From: Daniel Roe <daniel.r.roe.gmail.com>
Subject: Re: [AMBER] Problem in Radial command
To: AMBER Mailing List <amber.ambermd.org>
Content-Type: text/plain; charset=UTF-8


Why do you think the integration is poor? How large does the value of the
integration get? You have 128 methanol molecules - if your histogram is
large enough it should go up to 127. It's difficult to debug without more
details about what you think is wrong with the integration.

Also, you really should update to the latest version of cpptraj (15). The
new version contains many more features and bug fixes.


On Wed, Jun 24, 2015 at 11:43 PM, Robin Jain <robinjain.chem.gmail.com>

> Dear All amber users,
> I am simulating a organic molecule in 128 methanol and i want to calculate
> RDF between Methanol_oxygen to methanol_oxygen. For this i used following
> input.
> trajin x.mdcrd
> radial rdf-moh-O-O.dat 0.1 8 :MOH.O1 :MOH.O1 volume intrdf int-moh-o-o.dat
> go
> this input give good RDF but a very poor integration N(r) upto in hundreds
> . I am using CPPTRAJ 13.24 with all updates.What is the problem behind
> this. Please help me in this regard.
> Thanking You.
> --
> Robin Jain

Robin Jain
AMBER mailing list
Received on Thu Jun 25 2015 - 22:30:02 PDT
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