smd-tclForce intrerface

From: Jacqueline Schmidt (
Date: Wed Dec 26 2012 - 12:04:23 CST

Dear NAMD users, I trying to add an smd force on a group of atoms (a peptide). I have wrote my calcforces routine as below. The problem is the if statement (to get initial center of mass of my groups of atoms) does not work! I just need them for the force calculations, can anyone please help me! why the if { $t==0} (which must occur at the beginning of the simulation) does not work? set grp2 {} for {set j 1 } { $j <=107 } {incr j } { lappend grp2 $j } set a2 [addgroup $grp2] # set the output frequency, initialize the time counter set Tclfreq 50 set t 0 # force constant (kcal/mol/A^2) set k 10 # pulling velocity (A/timestep) set v 0.0001  set outfilename klpgwsg_smd_tcl.out open $outfilename w proc calcforces {} {   global Tclfreq t k v a2 c2x c2y c2z outfilename   loadcoords coordinate      if { $t==0 } { set r20 $coordinate($a2) set r20z [lindex $r20 2] #print    }   set r2 $coordinate($a2)   set r2x [lindex $r2 0]   set r2y [lindex $r2 1]   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]       set time [expr $t*2/1000.0]       puts $outfile "$time $r2z $f2z"       close $outfile   }   incr t   return }

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