[gmx-users] How to obtain the average radial density functions relative to the center of mass with g_rdf.

[Dallas Warren]

http://matdl.org/matdlwiki/index.php/softmatter:Radial_Distribution_Func
tion

 

That tells you what a rdf is and what the units are.

 

It is a probability function, so your graph is saying that you are 25
times more likely to find the tails 1 nm from the center versus in the
bulk.

 

If you want a density, then you are going to have to do some subsequent
processing to the data that the g_rdf script provides you.

 

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 sa
Sent: Tuesday, 1 March 2011 6:11 AM
To: gmx-users at gromacs.org
Subject: [gmx-users] How to obtain the average radial density functions
relative to the center of mass with g_rdf.

 

Dear GMXusers, 

Last week, i asked a question about the calculation of average radial
density functions relative to the center of mass of a micelle formed
with DPC molecules (rdf). Unfortunately i received no response. So i re
ask my question. So I would like to obtain the average rdf function (in
g/cm3) for different groups of my micellar system (such as the
headgroup, alkyl tail of the surfactant and water). For this purpose, I
have created a index file where all DPC atoms (heavy and H atoms ) are
separated in different groups and use the following command with g_rdf
(4.5.3)

g_rdf_mpi -f *_Center_All.xtc -s run_1.tpr -o
DPC-Self-AMB_100-155ns_DPC_RDF.xvg -b 100000 -e 155000 -norm -com -n
index_Radial_Profile_DPC.ndx 

I chose DPC atoms as a reference group and obtain the rdf curves for the
DPC headgroup, alkyl tail and water. I obtain the following figure : 

http://img4.hostingpics.net/pics/213680DPCSelfAMB100155nsRDF.jpg

I don't understand why the curves amplitudes for the headgroup, alkyl
tail are so high (and what is the unity ?),  For example for the C12
alkyl chain rdf  I understand well the help of the g_rdf tool, I expect
a rdf with a density maxima around 0.8 - 0.9 g/cm3. Did i compute the
expected function with above command ? If not, how to obtain the rdf (in
g/cm3) for each components ?

Thanks for the help. 

SA   

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