[gmx-users] coordinate number aroud the first shell

[mohammad agha]

Dear Prof.

Thank you very much for your reply.
Excuse me, I saw a figure in one article that showed the number density distribution for the surfactant molecules' angles for the production run. how? Is this as same as number density for coordinate number?how?
And some of articles with gromacs have a figure of radial density and radial number density and density as r(distance), I think those have been obtained with g_rdf, but how as a figure?  

Please help me.

Best Regards
Sara


________________________________
 From: Dallas Warren <Dallas.Warren at monash.edu>
To: Discussion list for GROMACS users <gmx-users at gromacs.org> 
Sent: Monday, December 12, 2011 12:38 AM
Subject: RE: [gmx-users] coordinate number aroud the first shell
 

 
1 – number of atoms divided by size of the box.
2 – manually or via a script.  I have a script set up within Sigma Plot that I use for mine, but can be done in any other spreadsheet and programming language too.
 
Catch ya,

Dr. Dallas Warren
Medicinal Chemistry and Drug Action
Monash Institute of Pharmaceutical Sciences, Monash University
381 Royal Parade, Parkville VIC 3010
dallas.warren at monash.edu
+61 3 9903 9304
---------------------------------
When the only tool you own is a hammer, every problem begins to resemble a nail.
 
From:gmx-users-bounces at gromacs.org [mailto:gmx-users-bounces at gromacs.org] On Behalf Of mohammad agha
Sent: Sunday, 11 December 2011 11:15 PM
To: gmx-users at gromacs.org
Subject: [gmx-users] coordinate number aroud the first shell
 
Dear Prof.
 
I want to obtain the coordinate number from the first shell around my cluster, I want to use from integration of the 4*pi*(number density)*area(g(r)r2dr) until the first minimum of the RDF, but I have some questions: Please help me
1- How do I obtain the number density for special rdf? by g_density? how?
2- After this, should I compute N (coordinate number) manually?
 
Best Regards
Sara
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