VMD-L Mailing List
From: Abhishek TYAGI (atyagiaa_at_connect.ust.hk)
Date: Mon Dec 26 2016 - 08:59:58 CST
Probably you are very excited, before posting this question, as posted several times.
Check the papers people recently published on CNT, you will get good idea about the bond lenght to be used.
And the mailing list have really good answers like this:
and tutorial like this:
Mailing list is the best resource for most of the questions.
all the best
From: owner-namd-l_at_ks.uiuc.edu <owner-namd-l_at_ks.uiuc.edu> on behalf of zeynab hoseyni <zmhoseyni_at_gmail.com>
Sent: Monday, December 26, 2016 8:45:28 PM
To: namd-l_at_ks.uiuc.edu; Vmd l
Subject: Fwd: namd-l: Modifying the equilibrium distance for a specific region of carbon nanotube in the parameter file
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 manually
but what about the equilibrium distance?
Would be so much thankful to guide me,
All the Best,