Re: Nanotube Simulation

From: Thomas C. Bishop (
Date: Mon Apr 14 2014 - 08:24:22 CDT

Thanks for directions Axel.

After digging into the topotools I used scripting to build all  kinds of nanotubes several months ago.
but never needed psf for my purposes.

The topoTools plugin page has all the info/examples needed.
animate write psf some.psf
is listed plain as day.
Reminder RTF(ree)M Tom... Axel put it there for a reason!

well done.

On 04/11/2014 02:55 PM, Axel Kohlmeyer wrote:
On Fri, Apr 11, 2014 at 3:44 PM, Thomas C. Bishop <> wrote:
I believe the scripts and tools that Axlel has for his
interactive sims of a nanotube -- bucky ball system might have what you

in the tar bundle is a parameter file and necessary info for doing the sims
w/ lamps and namd
BUT I agree w/ Miro I  don't actually see how Axel got the psf....   it
seems Topo tools were used and the nanotube builder gets you the pdb
but where's the psf...the nanobuilder gui says it's going to make one!
no it doesn't. the nanotube builder uses the topotools plugin to
generate topology data (bonds, angles, dihedrals and impropers) which
is then stored in VMD's memory. that is the whole point of most VMD
plugins, you use them to either feed VMD data or use the data to do
analysis. for writing out, you can just use the regular VMD commands.
the GUI can only do so many things. if you want to fully unleash the
power of VMD, you *have* to use the script interface. expecting a
"just click here" or "do you want this or that" kind of wizard
interface is too much effort to write and to inflexible. is it asking
too much to expect people to learn a little scripting and programming
of crucial tools they are using?

anyway, i usually don't have the patience to click through multiple
menus to write out files with the GUI and just use

animate writeXXX somefile.XXX ...


NOTE this  particular set of sims is great fun I use it for
education/outreach whenever I can.
.. SEE Axel;'s movies on youtube



On 04/11/2014 01:30 PM, Axel Kohlmeyer wrote:

On Apr 11, 2014 8:13 PM, "Miro Hodak" <> wrote:
Maybe this is too obvious, but I do not see it - and I have experience
with both NAMD and VMD.

I can save coordinates (pdb or other formats) once a nanotube is created,
but I see no way of getting a PSF file. I looked into the User's Guide and
tried the Automated PSF builder plugin, but I cannot figure this out.

If you can be more specific ...
Have you tried the script interface?

Thanks again,

On Fri, Apr 11, 2014 at 1:05 PM, Axel Kohlmeyer <>

On Apr 11, 2014 6:56 PM, "Miro Hodak" <> wrote:
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.
How to save files is explained in the vmd user's guide.

Thanks again,

On Fri, Apr 11, 2014 at 4:36 AM, Axel Kohlmeyer <>
On Thu, Apr 10, 2014 at 7:02 PM, Miro Hodak <>
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
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
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
College of Science & Technology, Temple University, Philadelphia PA,
International Centre for Theoretical Physics, Trieste. Italy.

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