[gmx-users] RDF of water

[Justin Lemkul]

On 7/31/13 12:18 PM, George Patargias wrote:
> Hi Justin
>
> Yes, it does look like Fig. 8.3 in the manual if I choose the OW atoms as
> the the two groups!
>
> So there must be a problem with the choice water-water or SOL-SOL for RDF
> groups.
>

Indeed there would, because then (with -rdf atom) you're calculating an RDF for 
all possible atom pairs when choosing whole molecules.

-Justin

 > Many thanks!
 >
>
>>
>>
>> On 7/31/13 10:49 AM, George Patargias wrote:
>>> Hello
>>>
>>> I am trying to calculate the RDF of water with water for a 10 ns MD of
>>> pure SPC water simulation (3x3x3 nm box). I run g_rdf with the default
>>> -rdf option (atom).
>>>
>>> The problem is that the integration of the RDF curve up to the first
>>> minimum yields a zero value which is obviously not right
>>>
>>> Do you have any suggestions about this? Should I run g_rdf in a
>>> different
>>> way?
>>>
>>
>> Impossible to tell without seeing the RDF itself.  If it doesn't look like
>> Figure 8.3 in the manual, then you've got a problem either with the
>> simulation
>> itself or the way the RDF was calculated.  If it does, then you've got a
>> problem
>> with how you're integrating the curve.
>>
>> -Justin
>>
>> --
>> ==================================================
>>
>> Justin A. Lemkul, Ph.D.
>> Postdoctoral Fellow
>>
>> Department of Pharmaceutical Sciences
>> School of Pharmacy
>> Health Sciences Facility II, Room 601
>> University of Maryland, Baltimore
>> 20 Penn St.
>> Baltimore, MD 21201
>>
>> jalemkul at outerbanks.umaryland.edu | (410) 706-7441
>>
>> ==================================================
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>
>
> Dr. George Patargias
> Postdoctoral Researcher
> Biomedical Research Foundation
> Academy of Athens
> 4, Soranou Ephessiou
> 115 27
> Athens
> Greece
>
> Office: +302106597568
>

-- 
==================================================

Justin A. Lemkul, Ph.D.
Postdoctoral Fellow

Department of Pharmaceutical Sciences
School of Pharmacy
Health Sciences Facility II, Room 601
University of Maryland, Baltimore
20 Penn St.
Baltimore, MD 21201

jalemkul at outerbanks.umaryland.edu | (410) 706-7441

==================================================