[gmx-users] Re: Calculation of coordination number for lithium ion

[Justin Lemkul]

Please keep all Gromacs-related questions on the gmx-user mailing list.  I am 
not a private tutor.

On 3/8/13 7:20 PM, QZG00677 at nifty.com wrote:
> Dear Dr. Justin
>
> Using g_rdf , I want to calculate coordination number of water molecule around Li+ in a Li
> salt aqueous solution. In order to calculate the radial distribution function, two Groups
> should be selected as 'Reference' and '1 group'. For the Li+ , which groups should I select
> among 0(system) -9(sideChain-H)?  I think that I should select System for Reference and
> again System for 1 group.  Is this correct?
>

A system-system RDF is likely useless.  If you want the RDF of water around 
lithium, it should be easy to select lithium as the reference group and water 
(or even better, OW atoms in an index group of your creation) as the group 
around that central group.  Selecting protein-related terms (i.e. within the 
first 10 default groups) makes no sense in light of what you're trying to measure.

-Justin

-- 
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Justin A. Lemkul, Ph.D.
Research Scientist
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu | (540) 231-9080
http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin

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