From: Jacqueline Schmidt (jacqueline_schmidt_1983_at_yahoo.com)
Date: Sun Feb 24 2013 - 13:02:21 CST
Dear NAMD users,
I am trying to use Tcl interface to add a steered MD velocity to a peptide. My system is running prior to SMD simulation for equilibration. Then I want to use the last configuration to pull my peptide 10 Ang upward.
For that purpose I want to calculate the center of mass of the peptide at the zeroth step of smd simulation (last configuration from the equilibration steps).
To do that, I am using a simple command "measure center $sel" at the beginning of my smd.tcl file (see below), but I get an error ** FATAL ERROR: wrong # args while executing "measure center $a2 weight mass **
can anyone please help me?
here is my smd.tcl
# defining a group which includes peptide atoms
set grp2 {}
for {set j 1 } { $j <=104 } {incr j } {
lappend grp2 $j
}
set a2 [addgroup $grp2]
# set the output frequency, initialize the time counter
set Tclfreq 10
set t 0
# force constant (kcal/mol/A^2)
set k 20
# pulling velocity (A/timestep)
set v 0.0000025
set outfilename rklpda_smd_tcl.out
open $outfilename w
##*******error happens here**************
set r20z [ lindex [ meausre center $a2 weight mass ] 2 ]
proc calcforces {} {
global Tclfreq t k v a2 r20z outfilename
loadcoords coordinate
set r2 $coordinate($a2)
set r2z [lindex $r2 2]
set f2x 0
set f2y 0
set f2z [expr $k*($v*$t-$r2z+$r20z)]
lappend f2 $f2x $f2y $f2z
addforce $a2 $f2
set foo [expr $t % $Tclfreq]
if { $foo == 0 } {
set outfile [open $outfilename a]
# calc time in ps
set time [expr $t]
puts $outfile "$time $r2z $f2z"
close $outfile
}
incr t
return
}
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