Re: Nanotube Simulation

From: Kenno Vanommeslaeghe (kvanomme_at_rx.umaryland.edu)
Date: Fri Apr 11 2014 - 17:18:18 CDT

There's one thing bugging me a bit in this discussion... The first
sentence in Miro's original post was: "I would like to run a NAMD
calculation of a nanotube interacting with a protein via non-bonded
interactions using CHARMM FF." I'm not familiar with the tools that were
mentioned in the subsequent answers, and would like to know what force
field / atom type is assigned to the nanotube. If it is an unofficial
extension of the CHARMM FF, what is the citation? And on what base is it
thought to interact correctly with a CHARMM protein?

On 04/11/2014 02:33 PM, MEHRAN MB wrote:
> 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
> <mailto: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
> <mailto:akohlmey_at_gmail.com>> wrote:
>
>
> On Apr 11, 2014 6:56 PM, "Miro Hodak" <mhodak127_at_gmail.com
> <mailto: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 <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
> >> > 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
> <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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