CST:Controls

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The behavior of constrained dynamics is controlled by the setup provided in the [cst] section. This section belongs to the {PMFLIB} group.

[cst]

Key	Default value	Type	Description
fmode	0	integer	The mode of constrained dynamics: 0 - the method is disabled 1 - the method is enabled If the method is enabled then at least one constraint should be provided in the {CST} group or in the external constraint definition file. The constraint specification is described in CST:Constraints.
freadranges	off	logical	Disable/Enable reading of CV ranges from the constraint definitions. If enabled, each CV must be accompanied by CV ranges (min_value, max_value, nbins).
fmdconmode	2	integer	The way how standard MD constraints are treated when they collide with CST constraints: 1 - MD constraints are excluded 2 - MD constraints are included
fmdcon_cvtype	0	integer	The CV type used for MD constraints included into the CST constraint list: 0 - DS 1 - DIS
fshakesolver	1	integer	The solver used for SHAKE constraint optimization: 0 - fixed SHAKE, LU solver 1 - mixed SHAKE, LU solver 2 - Newton-Raphson SHAKE, LL solver 3 - mixed SHAKE, diagonal solver 4 - mixed SHAKE, diagonal solver with initial guess from the previous step 5 - Newton-Raphson SHAKE, SVD solver 6 - Newton-Raphson SHAKE, LU solver
frattlesolver	0	integer	The solver used for RATTLE velocity correction: 0 - matrix algebra RATTLE
fshake_fdamp	0.0	real	Diagonal regularization used by selected SHAKE solvers.
frattle_fdamp	0.0	real	Diagonal regularization used by the RATTLE solver.
flamsol_fdamp	0.0	real	Diagonal regularization used for explicit lambda calculation.
ficf_fdamp	0.0	real	Diagonal regularization used by the ICF solver.
flambdatol	1.0^-7	real	Requested tolerance for SHAKE lambda optimization. The solution is accepted if all lambda corrections in the given step are lower than flambdatol.
frveltol	1.0^-9	real	Requested tolerance for the residual velocity in RATTLE/RATTLE-V velocity correction.
fmaxiter	50	integer	Maximum number of iterations that a constraint solver can use to find the solution of constraint equations.
fsample	2500	integer	Every fsample MD steps, the accumulated data are printed to the constrained dynamics output file. The name of the output file is provided in the [files] section. A value of 0 disables periodic output.
fplevel	0	integer	The level of output printed to the output file: 0 - standard output 1 - only user-specified constraints are printed
frestart	off	logical	Disable/Enable restarting the constrained dynamics simulation from the previous run. The name of the restart file is provided in the [files] section. If restart is enabled but no restart file exists, only a warning is raised.
faccurst	0	integer	After faccurst MD steps, the accumulated data are reset. This is useful for discarding the initial equilibration part of a simulation. A value of 0 disables this reset.
frstupdate	10000	integer	Every frstupdate MD steps, the constrained dynamics restart file is updated. A value of 0 disables periodic restart updates.
ftrjsample	0	integer	Every ftrjsample MD steps, the constrained dynamics trajectory data are written. The name of the trajectory file is provided in the [files] section. A value of 0 disables trajectory output.
flam_sample	1	integer	Every flam_sample MD steps, lambda and metric tensor corrections for free energy calculations are updated. The value must be greater than 0.
fintcalc	off	logical	Disable/Enable accumulation of data for internal energy calculation.
fint_der	off	logical	Disable/Enable accumulation of data for internal energy derivative calculation. If enabled, the ICF subsystem (VF (vector field) subsystem) is activated.
ftds_icfsol	1	integer	The solver used for the ICF contribution in internal energy/entropy calculations: 1 - V1, numerical divergence 2 - V2, analytical form with analytical/numerical CV Hessian and symmetry 3 - V3, stochastic divergence 4 - V1MW, numerical divergence with mass-weighted vector field 5 - V2MW, analytical form with analytical/numerical CV Hessian and symmetry with mass-weighted vector field 6 - V3MW, stochastic divergence with mass-weighted vector field
fpmf_sdiv_S	16	integer	Number of stochastic probe vectors used by the Hutchinson stochastic divergence estimator.
fpmf_sdiv_qr	off	logical	Disable/Enable QR orthonormalization of stochastic probe vectors used by the Hutchinson stochastic divergence estimator.
fpmf_sdiv_dh	1.0^-5	real	Finite-difference step factor used by the stochastic divergence estimator.
ftdscalc	off	logical	Disable/Enable accumulation of data for entropy calculation.
ftds_decomp	off	logical	Disable/Enable accumulation of additional correlation terms for entropy decomposition.
ftds_lamsol	0	integer	The source of lambda values used in entropy-related calculations: 0 - lambda values from the MD engine 1 - explicit lambda calculation
ftds_ekinsrc	1	integer	The source of kinetic energy used in entropy-related calculations: 0 - VV, velocity Verlet 1 - V4, fourth-order approximation 2 - V6, sixth-order approximation
fepotaverage	0.0	real	Expected average potential energy. The value is used as an energy offset in internal energy/entropy calculations.
fekinaverage	0.0	real	Expected average kinetic energy. The value is used as an energy offset in internal energy/entropy calculations.
ftds_sample	1	integer	Every ftds_sample MD steps, samples are taken for entropy and internal energy calculations. The value must be greater than 0.
frmmdcon_zdet	off	logical	Disable/Enable removal of MD constraints from the Fixman weight determinant.
fdump_data	off	logical	Disable/Enable dumping of extra internal energy and entropy-related data. The name of the dump file is provided in the [files] section.