Re: Nanotube Simulation

From: MEHRAN MB (mb.mehran1_at_gmail.com)
Date: Fri Apr 11 2014 - 13:33:31 CDT

Hi Miro,
I guess, you need to select your nano tube atoms then write pdb and psf
file.

like :
set mol [atomselect top "all resname CNT"]
$mol writepdb 1.pdb
$mol writepsf 1.psf

best,
Mehran
Uottawa

On Fri, Apr 11, 2014 at 1:13 PM, Miro Hodak <mhodak127_at_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 ...
>
> Thanks again,
> Miro
>
>
> On Fri, Apr 11, 2014 at 1:05 PM, Axel Kohlmeyer <akohlmey_at_gmail.com>wrote:
>
>>
>> On Apr 11, 2014 6:56 PM, "Miro Hodak" <mhodak127_at_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_at_gmail.com>
>> wrote:
>> >>
>> >> On Thu, Apr 10, 2014 at 7:02 PM, Miro Hodak <mhodak127_at_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_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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