From: snoze pa (snoze.pa_at_gmail.com)
Date: Mon Aug 10 2009 - 17:48:38 CDT
Or it pull it in a arbitrary direction. In the tutorial examples SMDir
is also not mentioned using constant force pulling.
On Mon, Aug 10, 2009 at 2:40 PM, snoze pa<snoze.pa_at_gmail.com> wrote:
> Dear NAMD Users,
>
> I was following the NAMD-SMD tutorials and found following lines in
> case of constant force pulling, page 69 of the latest tutorials.
>
> "The direction of the force will be specified in the coordinates of the SMD atom.
> Therefore, you have to write the normal vector in the following way:
> $smdatom set x nx
> $smdatom set y ny
> $smdatom set z nz
> where nx , ny , and nz have to be replaced by the appropriate values you already
> calculated above (in our example 0.443, 0.397, and 0.803). Since the VMD
> OpenGl Display interpretes the numbers just entered as coordinates of the SMD
> atom, it displays now a inaccurate protein structure. This is OK and
> we apologize
> for the poor appearance."
>
> Is it possible to do SMD using constant force pulling without VMD? (I
> think yes!) If yes then where and which file it write down following
> information?
>
> $smdatom set x nx
> $smdatom set y ny
> $smdatom set z nz
>
> I am unable to find any file where above numbers are written, except
> in VMD tcl console.
>
> Only information inf force.ref file I can find is:
>
> 1. The CA of First residues equal to 1 in B column and
> 2. CA of Last residue with force in B-column.
>
> Any Idea? I will highly appreciate your help.
>
> Thank You,
>
> S
>
>
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