From: Axel Kohlmeyer (akohlmey_at_gmail.com)
Date: Fri Apr 11 2014 - 17:41:04 CDT
On Fri, Apr 11, 2014 at 6:18 PM, Kenno Vanommeslaeghe
<kvanomme_at_rx.umaryland.edu> wrote:
> 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
the plugin only builds the geometry and the bond topology. most people
that i know are using the plugin (which is likely a very small subset)
then convert the geometry to a LAMMPS topology and use a manybody
potential to describe the CNT or graphene sheet. some dummy values are
assigned to make sure VMD writes out a valid file.
> citation? And on what base is it thought to interact correctly with a CHARMM
> protein?
the studies that i know about, use the atom type for a benzene carbon
(but they don't use CHARMM, but Amber (throughout)) and make the atoms
representing the CNT immobile or use a manybody potential like REBO or
AIREBO to describe the CNT structure itself. codes like LAMMPS allow
this kind of overlaying different potential types within certain
boundaries. sometimes also a Tersoff potential used.
axel.
>
>
>
> 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.
>> >
>> >
>>
>>
>>
>
-- 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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