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