a gap in flowing water

From: fereshteh moradi (f78moradi_at_gmail.com)
Date: Tue May 11 2010 - 06:45:31 CDT

Dear NAMD users

I have simulated the flow of water through a bundle of four nanotubes for
about 20 ns. The config file was prepared as namd tutorial, however, it was
unexpected to see a large distant blank (about 2 nm) between exiting water
molecules from nanotube and the down-stream bulk fluid. I have tried to
change pbc dimensions and also move molecules' center to origin (0 0 0), but
it didn't have any effect.
I reviewed the conf.file and saw that the only difference with namd
nanotubes tutorial is in force tcl part that I have changed it to become
more simple.
Here is the force tcl immersed in conf.file and I will be thankful if
somebody can take a look on it.

if {1} {

tclForces on
tclForcesScript {
  set force {0 0 0.01}
  set watIdList {}
  for {set i 1} {$i<3013} {incr i 3} {
    lappend watIdList $i
    addatom $i
  proc calcforces {} {
    global watIdList force
    loadcoords coorList
    foreach i $watIdList {
      set z [lindex $coorList($i) 2]
      if {$z<-2 || $z>12} {
        addforce $i $force

Please help me with some applicable hints, maybe I have forgotten some


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