Re: Nanotube Simulation

From: Thomas C. Bishop (bishop_at_latech.edu)
Date: Fri Apr 11 2014 - 14:44:08 CDT

I believe the scripts and tools that Axlel has for his
interactive sims of a nanotube -- bucky ball system might have what you need.

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!


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

https://www.youtube.com/user/templeicms

and
https://www.youtube.com/watch?v=JGz5oFR71jA




Cheers,
TOm


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


On Apr 11, 2014 8:13 PM, "Miro Hodak" <mhodak127@gmail.com> 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,
> Miro
>
>
> On Fri, Apr 11, 2014 at 1:05 PM, Axel Kohlmeyer <akohlmey@gmail.com> wrote:
>>
>>
>> On Apr 11, 2014 6:56 PM, "Miro Hodak" <mhodak127@gmail.com> 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,
>> > Miro
>> >
>> >
>> > On Fri, Apr 11, 2014 at 4:36 AM, Axel Kohlmeyer <akohlmey@gmail.com> wrote:
>> >>
>> >> On Thu, Apr 10, 2014 at 7:02 PM, Miro Hodak <mhodak127@gmail.com> 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?
>> >>
>> >> http://www.ks.uiuc.edu/Research/vmd/plugins/nanotube/
>> >>
>> >> >
>> >> > Thank you,
>> >> > Miro
>> >>
>> >>
>> >>
>> >> --
>> >> Dr. Axel Kohlmeyer  akohlmey@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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