RE: Nanotube Simulation

From: Samoylova, Olga M. (
Date: Tue Apr 15 2014 - 09:49:31 CDT

Hi Miro,
try this:

You can use the script make_arm.tcl to build armchair cnt (see tutorial

if you would like to use VMD nanotube builder, after you built cnt, open Tk console and type:
            animate write psf cnt.psf
            animate write pdb cnt.pdb

Then you may want to fix this psf and make cnt-xplor.psf (This is depends on version of VMD you using. In my case I had to do this. Thank you, Axel, I found this help in one of your mails in vmd-l mailing list). In Tk console:

             mol new cnt.psf waitfor all
             mol addfile cnt.pdb waitfor all

             set sel [atomselect top all]
             $sel set segid CNT

             animate write psf cnt-xplor.psf waitfor all
             animate write pdb cnt-xplor.pdb waitfor all

Next, you need to delete impropers from your psf file. Edit the line for impropers:
              0 !NIMPHI: impropers

Now your .psf ready for namd simulations.

PS. I have a question to more experienced audience. Am I right if I put 0 for impropers? I just compared the .psf files created by the script make_arm.tcl (no impropers) and psf file from vmd nanotube builder (which has improper parameters even if i didn't choose impropers in topology building options). If I try to run simulations with impropers I have error about these parameters. If I put 0 - everything works. I would appreciate any advice about it.

Thank you very much!



From: [] on behalf of Miro Hodak []
Sent: 11 April 2014 11:56
To: Axel Kohlmeyer
Cc: NAMD list
Subject: Re: namd-l: Nanotube Simulation

I know of that one, that is how I built my nanotube, but I do not see a way to get a PSF file from this plugin once the nanotube is built.

Thanks again,

On Fri, Apr 11, 2014 at 4:36 AM, Axel Kohlmeyer <<>> wrote:
On Thu, Apr 10, 2014 at 7:02 PM, Miro Hodak <<>> wrote:
> Dear all,
> I would like to run a NAMD calculation of a nanotube interacting with a
> protein
> via non-bonded interactions using CHARMM FF. This looks quite similar to
> what is
> done in a tutorial on water flow through nanotubes. However, that tutorial
> already provides a prebuilt PSF file for the nanotube used there. I want to
> work
> with a different nanotube (20,0) and looking at the tutorial and other
> resources
> I cannot figure out how to create a PSF file for an arbitrary nanotube I may
> want to work with.
> Can anybody help?

> Thank you,
> Miro

Dr. Axel Kohlmeyer<>
College of Science & Technology, Temple University, Philadelphia PA, USA
International Centre for Theoretical Physics, Trieste. Italy.

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