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

afsaneh maleki maleki.afsaneh at gmail.com
Tue Apr 30 09:25:28 CEST 2019

Hi all

I studied the insertion of one Drug inside a (10,10) CNT whose diameter is
equal to 13.56 Å.  I used

"g_rdf  –f md.xtc  –s md.tpr  –o rdf.xvg  –bin 0.03 " to calculate the RDF

I have three questions:

1-Is it need to add command  –pbc?

2- Whereas I have one Drug I don’t know how to explain this graph.  Do the
plot mean there is one pick (a broad peak at around 4.6- 9.2 Å   ) or two
sharp peak at 4.6 Å and 9.2 Å   ?

3-Since Diameter of CNT is 13.56 Å why do Drug had RDF value on wall of
diameter (13.56 Å)?

Can anyone help me?

Thanks in advance

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