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, qzg00...@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
--
========================================
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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