From: snoze pa (snoze.pa_at_gmail.com)
Date: Mon Aug 10 2009 - 14:40:51 CDT
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 speciļ¬ed 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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