Next: Adaptive Linear Bias/Experiment Directed Up: Biasing and analysis methods Previous: Harmonic wall restraints   Contents   Index

## Linear restraints

The linear restraint biasing method is used to minimally bias a simulation. There is generally a unique strength of bias for each CV center, which means you must know the bias force constant specifically for the center of the CV. This force constant may be found by using experiment directed simulation described in section . Please cite Pitera and Chodera when using [77].

• name: see definition of name (biasing and analysis methods)
• colvars: see definition of colvars (biasing and analysis methods)
• outputEnergy: see definition of outputEnergy (biasing and analysis methods)

• forceConstant Scaled force constant (kcal/mol)
Context: linear
Acceptable values: positive decimal
Default value: 1.0
Description: This option defines a scaled force constant for the linear bias. To ensure consistency for multidimensional restraints, it is divided internally by the specific width of each variable (which is 1 by default), so that all variables are effectively dimensionless and of commensurate size. See also the equivalent keyword for the harmonic restraint, forceConstant. The values of the actual force constants are always printed when the restraint is defined.

• centers Initial linear restraint centers
Context: linear
Acceptable values: space-separated list of colvar values
Description: These are analogous to the centers keyword of the harmonic restraint. Although they do not affect dynamics, they are here necessary to ensure a well-defined energy for the linear bias.

• writeTIPMF: see definition of writeTIPMF (biasing and analysis methods)
• writeTISamples: see definition of writeTISamples (biasing and analysis methods)

• targetForceConstant: see definition of targetForceConstant (Harmonic restraints)
• targetNumSteps: see definition of targetNumSteps (Harmonic restraints)
• targetForceExponent: see definition of targetForceExponent (Harmonic restraints)
• targetEquilSteps: see definition of targetEquilSteps (Harmonic restraints)
• targetNumStages: see definition of targetNumStages (Harmonic restraints)
• lambdaSchedule: see definition of lambdaSchedule (Harmonic restraints)
• outputAccumulatedWork: see definition of outputAccumulatedWork (Harmonic restraints)

Next: Adaptive Linear Bias/Experiment Directed Up: Biasing and analysis methods Previous: Harmonic wall restraints   Contents   Index
vmd@ks.uiuc.edu