From: Jim Pfaendtner (jpfaendt_at_hec.utah.edu)
Date: Sun Apr 27 2008 - 05:47:30 CDT
dear namd-l,
I am trying to apply a fixed force to a group of atoms in my protein
and have the direction of that force be defined by a vector between
two other atoms. The direction of the force is not applied correctly
and the group of atoms is not moving in the right direction. I think
I am doing something wrong with the loadcoords part of my TCL forces
script. I have pasted the essentials of the script below. Are there
any obvious problems?
set aid1 100
set aid2 200 #the vector between atom 100 and atom 200 defines the
direction of my force
addatom aid1
addatom aid2
set group [addgroup {1 2 3 4 5 6 ....}] #group contains all the atoms
to have force applied
set k 50
proc calcforces {} {
global aid1 aid2 group k
loadcoords p
#calculate normalized vector
set bondv [vecsub $p($aid2) $p($aid1)]
... normalize vector
set force [vecscale $k $bondv]
#apply forces
addforce $group $force
}
When I look at the simulation results the direction of motion of the
group of atoms does not seem to correspond to the vector defined in
the script. My guess is that I am doing something wrong with the
atoms/group and loading the coordinates.
I appreciate any suggestions!
Jim
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