Re: topology file for nanotube

From: Ranyere Deyler (
Date: Thu Mar 10 2011 - 02:10:13 CST

For simulating Nanotubes, you don't need a topology file. You just have to
use "topotools 1.1" that it can handle the creation of the psf file just
fine. Search for the help of the topotools 1.1 on google, and there you'll
find out how to obtain the psf file, you'll just tell it to guess the bonds,
angles and dihedrals, and then you just "writepdb" and "writepsf", and it's
good to run on NAMD. Take a look on the help!

Ranyere Deyler Trindade

On Thu, Mar 10, 2011 at 3:57 AM, sakthi kumaran <> wrote:

> Hi
> I am new to namd.I need to compute the free energy of a (5,5) nanotube
> in vacuum.So where can I get the topology file for the same.
> I also need clarifications of the following
> 1. Whether the topology file is different for different chirality of
> nanotubes.
> 2. whether the topology file is different when the medium chnges say vaccum
> to water.
> 3. whether the topolgy files for (5,5) and (10,10) nanotubes can be used
> together for (5,5)@(10,10) configuration.

This archive was generated by hypermail 2.1.6 : Mon Dec 31 2012 - 23:19:54 CST