Modifying the equilibrium distance for a specific region of carbon nanotube in the parameter file

From: zeynab mohamad hoseyni (
Date: Sun Dec 25 2016 - 12:46:28 CST

Dear All,

I want to simulate a hybrid carbon nano-tube (CNT) in water using CHARMM force field and NAMD code. By hybrid CNT I mean the CNT is composed of one (8,0) CNT in the middleand two (4,4) CNT connected on the both sides. As far as I know the parameters for carbon atoms of CNTs were those of type CA in the CHARMM force field, which was designed for benzene.Then the equilibrium distance should be about 1.37 A for pure CNT. But in the case of my hybrid CNT I need to change this parameters for the carbons located at the two interfaces of the hybrid CNT and possibly the related charges. Is there any way that I can modify the equilibrium distances of C-C bondsfor the mentioned interfaces? I assume that I change the partial charges for the interface regions in thepsf file manually but what about the equilibrium distance?
Would be so much thankful to guide me,All the Best,Zeynab

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