[gmx-users] Fwd: What could be wrong with rdf plot?

XAvier Periole x.periole at rug.nl
Sun Jan 3 13:18:29 CET 2010

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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