From: chengh_at_ringo.chem.pitt.edu
Date: Wed Dec 16 2009 - 08:40:37 CST
Dear NAMD developers and users,
Does anyone know how to get the system force on a fixed atom. I used
tclForces "loadtotalforces". It returned a value of zero. To solve this
problem, I used a very large homonic restraint (K=100000.0) to mimic
"fixed". Then using "loadforces" and "loadtotalforces" together to get the
system force. Any better solutions?
By the way, I noticed that "loadtotalforces" or "loadforces" did not work
using NAMD 2.7b1. I have to use an older version NAMD 2.6 to make it work.
I attached the script I used. Can anybody fix this problem in NAMD 2.7b1?
Many thanks,
Mary H. Cheng
Department of Chemistry
University of Pittsburgh
##############################################################################
tclForces on
tclForcesScript {
set aid1 168200
addatom $aid1
set Tclfreq 10
set k 100000.0
set x0 3.706
set y0 1.398
set z0 -26.642
proc calcforces {} {
global aid1 Tclfreq
global k z0 x0 y0
set t [getstep]
loadcoords r
set rx [lindex $r($aid1) 0]
set ry [lindex $r($aid1) 1]
set rz [lindex $r($aid1) 2]
print "COORDs: $t $r($aid1)"
addenergy [expr
$k*($rx-$x0)*($rx-$x0)/2.0+$k*($ry-$y0)*($ry-$y0)/2.0+$k*($rz-$z0)*($rz-$z0)/2.0]
set force "[expr -$k*($rx-$x0)] [expr -$k*($ry-$y0)] [expr
-$k*($rz-$z0)]"
addforce $aid1 $force
loadtotalforces fortot
loadforces forc
if { [array exists forc] } {
set f1 $forc($aid1)
set f1x [lindex $f1 0]
set f1y [lindex $f1 1]
set f1z [lindex $f1 2]
print "ADDforce: $t $f1x $f1y $f1z"
}
if
{
[array
exists
fortot]
}
{
set ftot $fortot($aid1)
set ftotx [lindex $ftot 0]
set ftoty [lindex $ftot 1]
set ftotz [lindex $ftot 2]
print "TOTforce: $t $ftotx $ftoty $ftotz"
print "SYSforce:$t [expr $ftotx-$f1x] [expr $ftoty-$f1y] [expr
$ftotz-$f1z]" }
}
}
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