Re: Distance Restraint

From: felmerino_at_uchile.cl
Date: Tue Nov 23 2010 - 13:12:23 CST

Hi Jacopo,

>From the error i guess that NAMD does not understand the -$force part, so it produces the "--17. something" number shown in the error which is not a floating point number. You should use something like vecscale $min * $force where min is -1. However, for a simple harmonic distance restraint i would use the colvars module. It is a lot less error prone.

best

Felipe

----Mensaje original----
De: sgrigna_at_sissa.it
Fecha: 23-11-2010 13:23
Para: <namd-l_at_ks.uiuc.edu>
Asunto: namd-l: Distance Restraint

Dear Namd users
i'm new to NAMD and i would like to use an harmonic restraint between to
atoms.
I found a script in this list:

# Scripting
# switch on tclforces
tclforces on
# Call tcl force

tclforcesScript {

# Set atom index
set at1 25371
set at2 8186
addatom $at1
addatom $at2

# Set costant force and eq. dist. V=-0.5*K(r-ro)^2
set k 050.0
set r0 6.000
print " TCLFORCE ACTION "

  # Call procedure
  proc calcforces {} {
  # set change variable
  global at1 at2 k r0
  # load coordinates
  loadcoords c
  # set distance for atom 1 and atom 2
  set r12 [vecsub $c($at2) $c($at1) ]
  set r [veclength $r12 ]
  # set unit vector
  set n0 [vecnorm $r12]
  # Force: F=-dV/dr
  set force [expr $k*($r-$r0)]

  # set vector force for atom 1 and atom 2
  set f1 [vecscale $force $n0 ]
  set f2 [vecscale -$force $n0 ]
  # add force f1 and f2 to atoms
  addforce $at1 $f1
  addforce $at2 $f2

}

# Ther is a definition of subroutine veclenght and vecnorm
# Returns: the vector length

proc veclength {v} {
  set retval 0
  foreach term $v {
          set retval [expr $retval + $term * $term ]
                  }
  return [expr sqrt($retval)]
}
# Returns: the normal vector
proc vecnorm {v} {
  set sum 0
  foreach term $v {
          set sum [expr $sum + $term*$term]
                  }
  set sum [expr sqrt($sum)]
  set retval {}
  foreach term $v {
          lappend retval [expr $term / $sum]
                  }
  return $retval
}
}

But now i get this error:

TCL: Running for 700 steps
TCL: expected floating-point number but got "--17.996288924"
FATAL ERROR: expected floating-point number but got "--17.996288924"
     while executing
"vecscale -$force $n0 "
     (procedure "calcforces" line 16)
     invoked from within
"calcforces"
------------- Processor 0 Exiting: Called CmiAbort ------------
Reason: FATAL ERROR: expected floating-point number but got
"--17.996288924"
     while executing
"vecscale -$force $n0 "
     (procedure "calcforces" line 16)
     invoked from within
"calcforces"

Could anybody help me?

Thanks

Jacopo

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