Re: Generating topology files for crystalline materials

From: Axel Kohlmeyer (akohlmey_at_gmail.com)
Date: Sun Feb 10 2013 - 16:05:16 CST

• Next message: Sahu, Indra: "Repelling extracellular regions of the protein from membrane in NAMD MD simulation"
• Previous message: FX: "Re: Generating topology files for crystalline materials"
• In reply to: FX: "Re: Generating topology files for crystalline materials"
• Messages sorted by: [ date ] [ thread ] [ subject ] [ author ] [ attachment ]

On Sun, Feb 10, 2013 at 10:58 PM, FX <fxcoudert_at_gmail.com> wrote:
>
> One final (I hope) question: is the list of bonds and dihedral required in the psf file, or can NAMD rebuild it itself? I ask because it could save me time to only write bonds and improper dihedrals.

i don't think so.

both psfgen and topotools should be able to build angles and dihedrals
from the bond topology.

axel.

> Thanks,
> FXC
>

-- 
Dr. Axel Kohlmeyer  akohlmey_at_gmail.com  http://goo.gl/1wk0
International Centre for Theoretical Physics, Trieste. Italy.

• Next message: Sahu, Indra: "Repelling extracellular regions of the protein from membrane in NAMD MD simulation"
• Previous message: FX: "Re: Generating topology files for crystalline materials"
• In reply to: FX: "Re: Generating topology files for crystalline materials"
• Messages sorted by: [ date ] [ thread ] [ subject ] [ author ] [ attachment ]

This archive was generated by hypermail 2.1.6 : Wed Dec 31 2014 - 23:20:54 CST