Yes of course but I was not sure g_rdf allowed it!
The solutions are actually explained in the g_rdf -h ...
On Jan 4, 2010, at 10:06 PM, Dallas B. Warren wrote:
Wouldn't it be simpler to just exclude the intramolecular -OHs when
you actually generate the RDF?
Catch ya,
Dr Dallas Warren
Pharmacy and Pharmaceutical Sciences
Monash University
A polar bear is a Cartesian bear that has undergone a polar
transformation
-----Original Message-----
From: gmx-users-boun...@gromacs.org on behalf of XAvier Periole
Sent: Tue 1/5/2010 6:33 AM
To: Discussion list for GROMACS users
Subject: Re: [gmx-users] Fwd: What could be wrong with rdf plot?
It is always better to keep the discussion in the list. Someone
could benefit of it as well as you from others.
From: Lum Nforbi <lumngwe...@gmail.com>
Date: January 4, 2010 7:57:04 PM GMT+01:00
To: XAvier Periole <x.peri...@rug.nl>
Subject: Thank you for reply on RDF PLOT problem/Question.
Hi Xavier,
Is there something I can do in order to eliminate this peak, maybe
like making adjustments to my coordinate file?
In your coordinates no, but you can just erase it. I am not actually
sure of
how the normalization of the rdf is done considering that this pick
should not
appear in the analyses!
Either someone else knows or you have to find out our self, looking at
the code
or in the archive :))
Thank you,
Lum
Message: 3
Date: Sun, 3 Jan 2010 13:18:29 +0100
From: XAvier Periole <x.peri...@rug.nl>
Subject: Re: [gmx-users] Fwd: What could be wrong with rdf plot?
To: Discussion list for GROMACS users <gmx-users@gromacs.org>
Message-ID: <28fdb30b-7b96-4975-bd1d-d6120f1b4...@rug.nl>
Content-Type: text/plain; charset="us-ascii"
I am not sure somebody gave you an answer ...
the first intense and probably very narrow pick is very
likely due to the intramolecular OH distance. It should be
around 0.1 nm, isn't it?
On Jan 1, 2010, at 3:53 AM, Lum Nforbi wrote:
---------- Forwarded message ----------
From: Lum Nforbi <lumngwe...@gmail.com>
Date: Thu, Dec 31, 2009 at 12:33 PM
Subject: What could be wrong with rdf plot?
To: gmx-users@gromacs.org
Dear all,
I am currently analyzing a system of 2000 molecules of TIP3P
water on which I performed a NPT simulation. The plot for g(OO)
looks very good but for some reason unknown to me, on the g(OH) plot
there is an intense peak coming before the normal peaks that are
characteristic of a g(OH) plot. Could someone tell me what is going
on? I have attached the graphs for gOO and gOH for viewing.
Also, I have still not been able to figure out how to calculate
the Cp of my system and I have been struggling with this for over a
month now. g_energy for my system gives a wrong Cv (~12). Can
someone explain to me or give me hints on how to calculate the Cp of
an NPT simulation of TIP3P water, please?
Have a wonderful New Year 2010 and Decade (2010-2019)!
Thank you,
Lum
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