Up: NAMD 2.9 User's Guide
- Graph of van der Waals potential with and without switching
- Graph of electrostatic potential with and without shifting function
- Graph of electrostatic split between short and long range forces
- Example of cutoff and pairlist distance uses
- Graph showing a slice of a ramp potential, showing the effect of
- Example of a collective variables (colvar) configuration.
The colvar ``'' is defined as the difference between two
distances, each calculated between the centers of mass of two
atom groups. The second colvar ``'' holds the coordination
number (i.e. the number of contacts) within a radius of 6 Å
between two groups. The third colvar ``alpha'' measures the
degree of -helicity of the protein segment between
residues 1 and 10. A moving harmonic restraint is applied to the
colvars ``'' and ``'', each rescaled by means of width
parameters and ; the centers of the restraint,
and , evolve with the simulation time . The joint
histogram of ``alpha'' and ``'' is also recorded on-the-fly.
- Dual topology description for an alchemical simulation.
Case example of the mutation of alanine into serine.
The lighter color denotes the non-interacting, alternate
- Convergence of an FEP calculation. If the ensembles representative
of states and are too disparate, equation (56) will
not converge (a).
If, in sharp contrast, the configurations of
state form a subset of the ensemble of configurations
characteristic of state , the simulation is expected
to converge (b).
The difficulties reflected in case (a) may be
alleviated by the introduction of mutually overlapping intermediate
states that connect to (c). It should be
mentioned that in practice, the kinetic contribution,
is assumed to be identical for state and state .
- Relationship of user-defined to coupling of electrostatic or vdW interactions to a simulation, given specific values of alchElecLambdaStart or alchVdwLambdaEnd.
- Sample TI data (
against ). The blue shaded
area shows the integral with fine sampling close to the end point. The red area
shows the difference when values are more sparse. In this example,
insufficient sampling before 0.1 can result in a large overestimation
of the integral. Beyond 0.2, sparser sampling is justified as dE/d is not
- Schematics of the aMD method. When the original potential (thick line) falls below a threshold energy (dashed line),
a boost potential is added. The modified energy profiles (thin lines) have smaller barriers separating adjacent