[gmx-users] RDF of water

[George Patargias]

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.

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