From: zeynab hoseyni (
Date: Mon Dec 26 2016 - 06:45:28 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 middle and 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 C-C bonds 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 bonds for the mentioned interfaces? I assume that I can
change the partial charges for the interface regions in the psf file
but what about the equilibrium distance?

Would be so much thankful to guide me,
All the Best,