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• writeXiFreq < Frequency at which the time series of ξ is written >
Acceptable Values: positive integer
Default Value: 0
Description: If this parameter is nonzero, the instantaneous value of the reaction coordinate, ξ, is written in the NAMD standard output every writeXiFreq time steps.
• distFile < Output file containing force distributions >
Acceptable Values: Unix filename
Default Value: none
Description: Output file containing a distribution of the instantaneous components of the
force, Fξ , for every bin comprised between xiMin and xiMax. This is useful for performing
error analysis for the resulting free energy profile
• fMax < Half–width of the force histograms >
Acceptable Values: positive decimal number, in kcal/mol/Å
Default Value: 60.0
Description: When force distributions are written in distFile, the histogram collects Fξ
values ranging from −fMax to +fMax.
• moveBoundary < Number of samples beyond which xiMin and xiMax are updated >
Acceptable Values: positive integer
Default Value: 0
Description: Slow relaxation in the degrees of freedom orthogonal to the reaction coordinate, ξ, results in a non–uniform sampling along the latter. To force exploration of ξ in quasi
non–ergodic situations, the boundaries of the reaction pathway may be modified dynamically
when a preset minimum number of samples is attained. As a result, the interval between
xiMin and xiMax is progressively narrowed down as this threshold is being reached for all
values of ξ. It should be clearly understood that uniformity of the sampling is artificial and
is only used to force diffusion along ξ. Here, uniform sampling does not guarantee the proper
convergence of the simulation.
• restraintList < Apply external restraints >
Acceptable Values: list of formatted entries
Default Value: empty list
Description: For a detailed description of this feature, see next subsection.
• applyBias < Apply a biasing force in the simulation ? >
Acceptable Values: yes or no
Default Value: yes
Description: By default, a biasing force is applied along the reaction coordinate, ξ, in ABF
calculations. It may be, however, desirable to set this option to no to monitor the evolution
of the system along ξ and collect the forces and the free energy, yet, without introducing any
bias in the simulation.
• usMode < Run umbrella sampling simulation ? >
Acceptable Values: yes or no
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