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Desmond Users Guide, Release 3.4.0 / 0.7.1
The improper dihedral angle phi is the angle between the plane ijk and jkl. Thus fc is in ENERGY and phi0 is in
RADIANS.
Table 7.14: Schema for the improper_fbhw table
name
fc
phi0
sigma
p0
p1
p2
p3
type
FLOAT
FLOAT
FLOAT
INTEGER
INTEGER
INTEGER
INTEGER
description
force constant in ENERGY/RADIANS2
equilibrium improper dihedral angle in DEGREES
half-width of flat-bottomed region in DEGREES
first particle
second particle
third particle
fourth particle
The functional form of the FBHW posre term is V = fc /2d2 where
(
|r − r0| − σ where |r − r0| > σ
d=
0
where |r − r0| <= σ
This is not as general as the fully harmonic position restraint term in that you can’t specify different force constants
for the three coordinate axes.
Table 7.15: Schema for the posre_fbhw table
name
fc
x0
y0
z0
sigma
p0
type
FLOAT
FLOAT
FLOAT
FLOAT
FLOAT
INTEGER
description
force constant in ENERGY/LENGTH2
equilibrium x coordinate in LENGTH
equilibrium y coordinate in LENGTH
equilibrium z coordinate in LENGTH
radius of flat-bottomed region in LENGTH
restrained particle
7.3 Van der Waals and electrostatic interactions
The nonbonded forces are configured as shown in:
force.nonbonded = {
n_zone = nz
sigma = σ
r_cut = Rcut
near = {
type = near-type
...
}
far = {
type = far-type
...
}
}
Van der Waals interactions decay rapidly with distance, whereas electrostatic interactions are split into a rapidly decaying part (near) and a slowly decaying part (far). Near nonbonded interactions are computed by summing them over
all pairs (except the excluded ones) within a distance Rcut of each other. Far electrostatic interactions are computed
by an Ewald summation technique specified in the far configuration (see Nonbonded far interactions) and a sum over
certain designated electrostatic correction terms.
7.3. Van der Waals and electrostatic interactions
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