From: Miro Hodak (mhodak127_at_gmail.com)
Date: Fri Apr 11 2014 - 13:13:32 CDT
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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