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

[XAvier Periole]

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-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
> 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.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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