VMD-L Mailing List

From: Tim Lo (timlo_at_connect.hku.hk)
Date: Fri Dec 29 2017 - 20:38:47 CST

Dear Suresh,

To combine water and carbon nanotube into a single psf file, the most
convenient way is to use mergemols of TopoTools. Please read the
tutorial at
https://sites.google.com/site/akohlmey/software/topotools/topotools-tutorial---part-2.
Water and carbon nanotube don't require any improper interaction, so
just write "0 !NIMPHI: impropers" in the improper section of the merged
psf file.

Regards,

Tim

Research Associate

The University of Hong Kong

On 26/12/2017 12:29, Suresh Ghimire wrote:
> Dear VMD users,
>  I am trying to build psf file combine to water and carbon nanotube,
> how can I do that? and how can we set improper 0 for nanotube?
>
> On Mon, Dec 18, 2017 at 9:47 PM, John Stone <johns_at_ks.uiuc.edu
> <mailto:johns_at_ks.uiuc.edu>> wrote:
>
> Your best options are either to use the nanotube builder plugin
> included with VMD, or to learn how to use psfgen and build it yourself
> if you want to do something that the existing nanotube builder
> can't handle.
>
> Best,
>   John Stone
> vmd_at_ks.uiuc.edu <mailto:vmd_at_ks.uiuc.edu>
>
> On Sun, Dec 17, 2017 at 06:42:45PM +0545, Suresh Ghimire wrote:
> >    how can we build the PSF file for nanotube?
>
> --
> NIH Center for Macromolecular Modeling and Bioinformatics
> Beckman Institute for Advanced Science and Technology
> University of Illinois, 405 N. Mathews Ave, Urbana, IL 61801
> http://www.ks.uiuc.edu/~johns/ <http://www.ks.uiuc.edu/%7Ejohns/>
>          Phone: 217-244-3349 <tel:217-244-3349>
> http://www.ks.uiuc.edu/Research/vmd/
> <http://www.ks.uiuc.edu/Research/vmd/>
>
>