Re: vmd-l: Nanotube Simulations

From: Jordi Cohen (
Date: Tue Aug 02 2005 - 14:41:03 CDT


I am currently in charge of the nanotubes tutorial, however I did not
develop the nanotubes "simulation" part of it and I cannot answer
your question with certainty. I believe that the parameters for the
nanotube carbon atoms were simply taken from the CHARMM force-field's
alpha carbons, so nothing fancy. This would probably work acceptably
if you simply want to have nanotubes in your simulation cell, but
would definitely fail if you wanted to measure quantitative
properties such as elastic moduli under strain, etc.

I am not familiar with Brenner's hydrocarbon potential, however as
long as the potential consists only of angular constraints, harmonic
spring constraints and dihedral constraints in the same form as the
CHARMM force-field, then it would be trivial to implement that by
filling in the right constants in the parameter file.


On Aug 2, 2005, at 1:56 PM, Gaurav Sharma wrote:

> Hi John,
> Yes, I have run some of those simulations when I attended the NAMD
> wokshop at Boston last year. What I am not sure is that whether the
> tutorial parameter files includes the Brenner's hydrocarbon
> potential for nanotubes. We didn't simulate the nanotube atoms in
> the tutorial (all of them were fixed), we just simulated the water
> permeation through them. I want to run simulations where I can
> stretch, pull, strain the nanotube by applying external force.
> Please let me know if the tutorial parameter file contains the
> brenner's potential or else where can I find those files.
> Thanks in advance.
> Gaurav
> John Stone wrote:
>> Hi, Have you had a look at the Nanotube tutorial on our web site?
>> nanotubes.pdf
>> nanotubes/nanotubes-html/index.html The data files that go with
>> that tutorial include parameter files for the nanotubes in the
>> tutorial:
>> nanotubes/files/
>> nanotubes/nanotubes-tutorial-files.tar.gz Hope that helps, John
>> Stone On Tue, Aug 02, 2005 at 09:51:14AM -0400,
>> Gaurav Sharma wrote:
>>> Hi All, I have posted a similar question on the list before but
>>> met with no response. Here is a simpler version: Is it possible
>>> to do molecular mechanics simulations on carbon nanotubes using
>>> NAMD? If yes, where can I find the required parameter and
>>> topology files containing the appropriate (brenner's) force field
>>> potential? Any suggestions are welcome. Thanks, Gaurav

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