NAMD provides a limited Tcl scripting interface designed for applying forces and performing on-the-fly analysis. This interface is efficient if only a few coordinates, either of individual atoms or centers of mass of groups of atoms, are needed. In addition, information must be requested one timestep in advance. To apply forces individually to a potentially large number of atoms, use tclBC instead as described in Sec. 9.11. The following configuration parameters are used to enable the Tcl interface:
is Tcl interface active? 
input for Tcl interface
At this point only low-level commands are defined. In the future this list will be expanded. Current commands are:
print Hello World''.
Å
) into a local array.
loadforces should only be called from within the calcforces procedure.
For example, ``loadforces f'' and ``print $f(4)''.
Å
) into a local array. The
total force also includes external forces. Note that the
``loadforces'' command returns external forces applied by
the user. Therefore, one can subtract the external force on an
atom from the total force on this atom to get the pure force
arising from the simulation system.
Å
) to atom or group.
addforce should only be called from within the calcforces procedure.
For example, ``addforce $groupid { 1. 0. 2. }''.
With the commands above and the functionality of the Tcl language, one should be able to perform any on-the-fly analysis and manipulation. To make it easier to perform certain tasks, some Tcl routines are provided below.
Several vector routines (vecadd, vecsub, vecscale) from the VMD Tcl interface are defined. Please refer to VMD manual for their usage.
The following routines take atom coordinates as input, and return some geometry parameters (bond, angle, dihedral).
The following routines calculate the derivatives (gradients) of some geometry parameters (angle, dihedral).
(in radian).
This command takes the coordinates of the three atoms as input,
and returns a list of {
}. Each element of the
list is a 3-D vector in the form of a Tcl list.
(in
radian). This command takes the coordinates of the four atoms as
input, and returns a list of
{
}. Each element of the
list is a 3-D vector in the form of a Tcl list.
As an example, here's a script which applies a harmonic constraint (reference position being 0) to a dihedral. Note that the ``addenergy'' line is not really necessary - it simply adds the calculated constraining energy to the MISC column, which is displayed in the energy output.
tclForcesScript {
# The IDs of the four atoms defining the dihedral
set aid1 112
set aid2 123
set aid3 117
set aid4 115
# The "spring constant" for the harmonic constraint
set k 3.0
addatom $aid1
addatom $aid2
addatom $aid3
addatom $aid4
set PI 3.1416
proc calcforces {} {
global aid1 aid2 aid3 aid4 k PI
loadcoords p
# Calculate the current dihedral
set phi [getdihedral $p($aid1) $p($aid2) $p($aid3) $p($aid4)]
# Change to radian
set phi [expr $phi*$PI/180]
# (optional) Add this constraining energy to "MISC" in the energy output
addenergy [expr $k*$phi*$phi/2.0]
# Calculate the "force" along the dihedral according to the harmonic constraint
set force [expr -$k*$phi]
# Calculate the gradients
foreach {g1 g2 g3 g4} [dihedralgrad $p($aid1) $p($aid2) $p($aid3) $p($aid4)] {}
# The force to be applied on each atom is proportional to its
# corresponding gradient
addforce $aid1 [vecscale $g1 $force]
addforce $aid2 [vecscale $g2 $force]
addforce $aid3 [vecscale $g3 $force]
addforce $aid4 [vecscale $g4 $force]
}
}