[gmx-users] How can i calculate RDF of one capsulated Drug in Carbon nanotube (CNT) simulated?

Dallas Warren dallas.warren at monash.edu
Tue Apr 30 23:20:46 CEST 2019

1 - pbc is on by default, so there is no need to use that command switch
unless you want to shut it off.

2 - no idea since we can't see the graph. You need to load it somewhere
that we can access it via a URL to look at it.

3 - can't say because you have no told us what the rdf is actually
calculated between ie atoms, center of mass of a molecule etc. groups that
you selected when you executed the command.

On Tue, 30 Apr. 2019, 5:14 pm afsaneh maleki, <maleki.afsaneh at gmail.com>

> I studied the insertion of one Drug inside a (10,10) CNT whose diameter is
> equal to 13.56 Å. Attached is the RDF of CNT around Drug. I used
> "g_rdf  –f md.xtc  –s md.tpr  –o rdf.xvg  –bin 0.03 " to calculate the RDF
> .
> I have two questions:
> 1-Is it need to add command  –pbc?
> 2- Does the plot mean that there is one pick (a broad peak at around 4.6-
> 9.2 Å   ) or two sharp peak whereas I have one Drug?
> 3-Since Diameter of CNT is 13.56 Å why do Drug had RDF value on wall of
> diameter (13.56 Å)?
> Thanks in advance
> [image: image.png]
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