[gmx-users] rdf problem

[Dallas B. Warren]

If you have aggregation and a small box size, then the rdf will not be
able to asymptote to one.

 

Catch ya,

Dr. Dallas Warren
Drug Delivery, Disposition and Dynamics
Monash Institute of Pharmaceutical Sciences, Monash University
381 Royal Parade, Parkville VIC 3010
dallas.warren at pharm.monash.edu.au
+61 3 9903 9167
---------------------------------
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 Antonia V.
Sent: Thursday, 11 March 2010 2:18 AM
To: gmx-users at gromacs.org
Subject: [gmx-users] rdf problem

 

Dear all,

I am simulating a binary system of two non mixing components (5CB and
water using version 4-0-3; the whole equilibrated trajectory is about
300ns). 
I want to calculate the rdf of the centers of mass of 5CB using the
command 
g_rdf -f traj300.xtc -rdf mol_com  -o rdf_com_300.xvg -noxvgr.
The problem is that the rdf I am getting does not approach one at long
distances. Is there a way to correct that? 
I have the same problem, with all rdfs, and also when I compute the rdfs
for a lipid bilayer (DPPC-water)... I think it has to do with the way
that the normalization is done, 
because the ones that are calculated for a one component system (i.e.
bulk 5CB) are normal (they do approach one). 

Thank you,
Antonia

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