Re: questions about set cellBasisVector and a ligand ...

From: Edward Patrick Obrien (
Date: Thu Apr 29 2004 - 12:59:15 CDT

On Thu, 29 Apr 2004, Xiaobing Tian wrote:

> Dear everyone,
> I started to do MD using namd. But there are several questions I am not
> sure.
> 1. How do I set cellBasisVector1,2 and 3 for a specific protein?
> There are not instructions about this in both namd manual and tutorial.

   There are instructions in the tutorial, 'Statistical Mechanics of
Proteins'. Go through it. Basically in VMD you must measure the minmax of
the cell and calc your basis vectors from that, and then put them in your
namd configuration file.

   In VMD: >set everyone [atomselect top all]
>measure minmax $everyone
   To select the protein: >set protein [atomselect top protein]
>measure minmax $protein

   Go through the tutorial for more info.


This archive was generated by hypermail 2.1.6 : Wed Feb 29 2012 - 15:37:33 CST