[gmx-users] spatial distribution function (SDF)

Dallas B. Warren Dallas.Warren at pharm.monash.edu.au
Fri Dec 4 01:11:35 CET 2009

First three groups are the reference group, from which the SDF is generated, it sets the coordinate system.  That means you need to have at least three "atoms" in the "molecule" you are generating the SDF from.

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 naimah haron naimah
Sent: Thu 12/3/2009 9:03 PM
To: gromacs
Subject: [gmx-users] spatial distribution function (SDF)
Hai all...

Did anyone know how to do spatial distribution functions??? I have 125 ion pairs in my system. The problem is, 

1)how I can I get the 3-D probability distributions of anion around cation or cation around anion in my system? Could anybody tell me the method? 
2)When I read the GROMACS manual, I should create 4 group in my index file. Can anybody tell me what is first, second, three and for group represent??? I already try to do it, but  I'm failed to get the result.. 




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