Re: How to set magnitude of cellBasisVector?

From: Joshua Adelman (jadelman_at_berkeley.edu)
Date: Fri Jul 24 2009 - 01:13:24 CDT

Hi Aurum,

This question has been addressed on the list before. A simple search
of the archive will provide you an answer. See the following thread
for starters (but it is worth reading through more of them for
additional details):
http://www.ks.uiuc.edu/Research/namd/mailing_list/namd-l/1160.html

Josh

On Jul 23, 2009, at 10:52 PM, Aurum Bai wrote:

> Hello everyone.
>
> I do the namd simulation,but some parameter should be consider
> carefully.
> I want to ask question as below:
>
> # Periodic Boundary Conditions
> cellBasisVector1 42. 0. 0.
> cellBasisVector2 0. 44. 0.
> cellBasisVector3 0. 0 47.
> cellOrigin 31. 29. 17.5
>
> The cellOrigin is the center of box, it can be sure by the vmd
> "measure center $ everyone"
>
> However, how to get the magnitude of "cellBasisVector"?
> And which factors decide the dimension of the "cellBasisVector" ?
>
> Thanks!
> Aurum
>
>
>
>

This archive was generated by hypermail 2.1.6 : Wed Feb 29 2012 - 05:22:15 CST