[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 09:14:04 CEST 2019

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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