From: Arturas Ziemys (ziemys_at_chbmeng.ohio-state.edu)
Date: Wed Nov 22 2006 - 14:55:36 CST
Hi,
My system contains water, sodium ion, chlorine ion and dummy particle. I introduce the repulsive potential acting from dummy particle onto sodium ions. I add force acting away from dummy JUST on sodium ion and the repulsive force decreases then sodium ions get further from dummy particles: the aim was to create the force moving them away from dummy particle.
I realized that dummy moves with "cosmic" speeds, but sodium ions are "lazy". My dummy particle has mass 0. I expected that my dummy particle - having no interactions and with zero mass - will remain , where I places at the beginning.
Would appreciate some comments and advices. Here is the main peace of my Tcl script below.
Arturas
Script:
==============================================
set D1 680 ;# ID of dummy
set Na1 670 ;# ID of sodium
set Na2 671
set Na3 672
set Na4 673
set Na5 674
addatom $D1
addatom $Na1
addatom $Na2
addatom $Na3
addatom $Na4
addatom $Na5
set r0 5
set k 2.0
proc calcforces {} {
global D1
global Na1 Na2 Na3 Na4 Na5
global k
global r0 5
loadcoords Coor
set c0 $Coor($D1)
foreach Na [list $Na1 $Na2 $Na3 $Na4 $Na5] {
set n0 [list]
set c $Coor($Na)
set r [vecsub $c $c0]
set len [getbond $c $c0]
lappend n0 [expr [lindex $r 0]/$len] [expr [lindex $r 1]/$len] [expr [lindex $r 2]/$len]
set f [expr $k/($len)]
addforce $Na $fc
}
}
==============================================
This archive was generated by hypermail 2.1.6 : Wed Feb 29 2012 - 15:42:51 CST