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Desmond Users Guide, Release 3.4.0 / 0.7.1
Table 4.10: Configuration for BiasingForce
name
cm_moi
groups
displace_coeff
displacement
distance_coeff
distance
orient_coeff
Euler_angles
use_lab_frame_for_displacement
pull_displacement
pull_distance
pull_Euler
t0
output.first
output.interval
output.name
description
Biasing force definition for a list of cm_moi groups [List]
The groups to restrain [List]
Force coefficients for displacement restraints [List of 3
Energy/Length2 ]
Relative displacement between the two groups [List of 3 Lengths]
Force coefficient for distance restraint [Energy/Length2 ]
Distance between the two groups [Length]
Force coefficients for orientational restraints [List of 3 Energies]
Euler angles between the two groups [List of 3 Degrees]
If true, the displacement between the groups are measured in the
reference frame of the simulation box [Boolean]
Velocity of pulling in displacement [List of 3 Length/Time]
Velocity of pulling in distance [Length/Time]
Velocity of pulling in orientation [List of 3 Degree/Time]
The time to begin apply pulling, as specified by
pull_displacement, pull_distance, and pull_Euler. This is not to be
confused with the biasing force itself, which is applied from the
beginning of the simulation. [Time]
The time to write the first biasing results [Time]
The interval at which to write the biasing results [Time]
The name of the file to which to write the energy estimates
[Filename]
4.6.3 e_bias
The e_bias plugin applies a constant electric field with the direction and magnitude given by E_applied. The
schedule subsection can be set to none; if so, the field remains constant over time; otherwise, it’s scaled by the
values given in schedule.value.
force.term = {
list = [ ... key ... ]
key = {
type = e_bias
E_applied = [Ex Ey Ez ] # Applied field in kcal/mol/A/e
schedule = {
time = [ t1 t2 ... tN ] # Times in picosecond
value = [ S1 S2 ... SN ]
}
}
... # other force terms
}
With e_bias, a particle carrying charge q experiences a force
F~ = (qEx (t), qEy (t), qEz (t))
where the electric field at time t is given by Eα (t) = Eα S(t)forα = x, y, z
The time-dependent scaling factor S(t) is determined by the schedule. If schedule=none, then S(t) = 1 for all t.
4.6. Configuring the built-in plugins
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