General setup

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General setup of PMFLib can be controlled by following sections specified in the {PMFLIB} group. They control behaviour of PMFLib core, define units used for input data specification and names of input and output files.

[control]

Key	Default value	Type	Description
ftopology	system topology	string	The name of file with a system topology in AMBER7 format. If provided the loaded topology will be used during ASL masks processing instead of the system topology.
fdebug	off	logical	If enabled it prints debugging information if they are available.
fprint_masks	off	logical	If enabled it prints detailed information about atoms in each ASL masks.
fprint_inpcrds	off	logical	If enabled it prints input coordinates inluding atom and residues names and indexes.
fenable_pbc	off	logical	If enabled then the periodic boundary conditions are used whenever possible. Please note that not all collective variables are influenced by this option.

[units]

Key	Default value	Type	Description
mass	g/mol	string	unit of molar mass Allowed values are : g/mol
time	fs	string	unit of time Allowed values are : fs
length	A	string	unit of length Allowed values are : A
angle	rad	string	unit of angle Allowed values are : deg, rad
energy	kcal/mol	string	unit of energy Allowed values are : kcal/mol

Units provided here are used only for input parameters and for output data printed into output files. Other data printed into restarts or other internal files still use internal units.

[files]

Key	Default value	Type	Description
Adaptive Biasing Force Method
fabfdef	{ABF}	string	It defines either a PRMFile group or a file name containing the specification of collective variables used by the ABF method.
fabfout	_abf.out	string	It defines a file name used as output from ABF method simulations. This file contains status information and the progress of collective variables in time.
fabfrst	_abf.rst	string	It defines the name of file with accumulated results from ABF simulations.
fabftrj	_abf.trj	string	It defines the name of file which contains time evolution of accumulated ABF results.
fabfmask	_abf.mask	string	It defines the name of file that contains ABF force weights.
Constrained Dynamics
fcondef	{CON}	string	It defines either a PRMFile group or a file name containing the specification of constraints.
fconout	_con.out	string	It defines a file name used as output from constrained dynamics simulations. This file contains status information and the progress of calculation in time.
fconrst	_con.rst	string	It defines the name of file with results from the constrained dynamics simulation. This file is solely used for constrained dynamics calculation restarts.
Metadynamics
fmtddef	{MTD}	string	It defines either a PRMFile group or a file name containing the specification of metadynamics collective variables.
fmtdout	_mtd.out	string	It defines a file name used as output from the metadynamics method. This file contains status information and the progress of collective coordinates in time.
fmtdrst	_mtd.rst	string	It defines the name of file containg accumulated gaussian hills from metadynamics simulations.
fmtdcvs	_mtd.cvs	string	It defines the name of file containg accumulated gaussian hills from metadynamics simulations. This file together with fmetahills file contain the same information as fmetarst.
fmtdhills	_mtd.hills	string	It defines the name of file containg accumulated gaussian hills from metadynamics simulations. This file together with fmtdcvs file contain the same information as fmtdrst.
Restrained Dynamics
fresdef	{RST}	string	It defines either a PRMFile group or a file name containing the specification of restraints used in restrained dynamics simulations.
fresout	_rst.out	string	It defines a file name used as output from restrained dynamics simulations This file contains status information and the progress of restrained collective variables in time.
fresrst	_rst.rst	string	It defines the name of file with accumulated results from restrained dynamics simulations. This file contains run-time histogram of collective variables (density function).
String Method
fstmdef	{STM}	string	It defines either a PRMFile group or a file name containing the specification of collective variables used by the string method.
fstmout	_stm.out	string	It defines a file name used as output from string method simulations.
Collective Variable Monitoring
fmondef	{MON}	string	It defines either a PRMFile group or a file name containing the specification of collective variables used during monitoring.
fmonout	_mon.out	string	It defines a file name used as output from the collective variable monitoring.