[gmx-users] Fwd: What could be wrong with rdf plot?
Dallas B. Warren
Dallas.Warren at pharm.monash.edu.au
Mon Jan 4 22:06:26 CET 2010
Wouldn't it be simpler to just exclude the intramolecular -OHs when you actually generate the RDF?
Dr Dallas Warren
Pharmacy and Pharmaceutical Sciences
A polar bear is a Cartesian bear that has undergone a polar transformation
From: gmx-users-bounces at 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 <lumngwegia at gmail.com>
> Date: January 4, 2010 7:57:04 PM GMT+01:00
> To: XAvier Periole <x.periole at 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
how the normalization of the rdf is done considering that this pick
appear in the analyses!
Either someone else knows or you have to find out our self, looking at
or in the archive :))
> Thank you,
> Message: 3
> Date: Sun, 3 Jan 2010 13:18:29 +0100
> From: XAvier Periole <x.periole at rug.nl>
> Subject: Re: [gmx-users] Fwd: What could be wrong with rdf plot?
> To: Discussion list for GROMACS users <gmx-users at gromacs.org>
> Message-ID: <28FDB30B-7B96-4975-BD1D-D6120F1B4BEA at 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 <lumngwegia at gmail.com>
> > Date: Thu, Dec 31, 2009 at 12:33 PM
> > Subject: What could be wrong with rdf plot?
> > To: gmx-users at 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
> > <RDF_OWHW1HW2_0_8000PS>--
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