From: Samoylova, Olga M. (Olga_Samoylova_at_baylor.edu)
Date: Tue Apr 15 2014 - 09:49:31 CDT
You can use the script make_arm.tcl to build armchair cnt (see tutorial http://www.ks.uiuc.edu/Training/Tutorials/science/nanotubes/)
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: owner-namd-l_at_ks.uiuc.edu [owner-namd-l_at_ks.uiuc.edu] on behalf of Miro Hodak [mhodak127_at_gmail.com]
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.
On Fri, Apr 11, 2014 at 4:36 AM, Axel Kohlmeyer <akohlmey_at_gmail.com<mailto:akohlmey_at_gmail.com>> wrote:
On Thu, Apr 10, 2014 at 7:02 PM, Miro Hodak <mhodak127_at_gmail.com<mailto:mhodak127_at_gmail.com>> wrote:
> Dear all,
> I would like to run a NAMD calculation of a nanotube interacting with a
> 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
> with a different nanotube (20,0) and looking at the tutorial and other
> 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,
-- Dr. Axel Kohlmeyer akohlmey_at_gmail.com<mailto:akohlmey_at_gmail.com> http://goo.gl/1wk0 College of Science & Technology, Temple University, Philadelphia PA, USA International Centre for Theoretical Physics, Trieste. Italy.
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