General setup

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The general setup of PMFLib can be controlled through the following sections in the {PMFLIB} group. These sections control the behaviour of the PMFLib core ([control]), define the units used for input/output data specification ([units]), and specify the names of input and output files ([files]).

[control]

Key	Default value	Type	Description
ftopology	system topology	string	Specifies the name of a file with the system topology in AMBER7 format. If provided, the loaded topology is used during ASL mask processing instead of the system topology.
fdebug	off	logical	If enabled, prints debugging information if available.
fprint_masks	off	logical	If enabled, prints detailed information about atoms in each ASL mask.
fprint_inpcrds	off	logical	If enabled, prints input coordinates, including atom and residue names and indexes.
fenable_pbc	off	logical	If enabled, 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	Specifies the unit of molar mass. Allowed values are: au, a.u., g/mol, amu
time	fs	string	Specifies the unit of time. Allowed values are: au, a.u., fs, ps
length	A	string	Specifies the unit of length. Allowed values are: au, a.u., A, pm, nm
angle	deg	string	Specifies the unit of angle. Allowed values are: rad, deg
energy	kcal/mol	string	Specifies the unit of energy. Allowed values are: au, a.u., eV, kcal/mol, kJ/mol
temperature	K	string	Specifies the unit of temperature. Allowed values are: K
pressure	Pa	string	Specifies the unit of pressure. Allowed values are: Pa, kPa

Units specified in this section are used only for input parameters and for data written to output files. Data written to restart files or other internal files are still stored in internal units.

[files]

Key	Default value	Type	Description
Collective Variables / Paths
fcvsdef	{CVS}	string	Specifies either a PRMFile group or the name of a file containing the collective variable specification.
fpathsdef	{PATHS}	string	Specifies either a PRMFile group or the name of a file containing the path specification.
Adaptive Biasing Force Method
fabfdef	{ABF}	string	Specifies either a PRMFile group or the name of a file containing the specification of collective variables used by the ABF method.
fabfmask	_abf.mask	string	Specifies the name of the file containing ABF force weights.
fabfout	_abf.out	string	Specifies the file name used for output from ABF simulations. This file contains status information and the progress of collective variables in time.
fabfrst	_abf.rst	string	Specifies the name of the file containing accumulated results from ABF simulations.
fabftrj	_abf.trj	string	Specifies the name of the file containing the time evolution of accumulated ABF results.
Adaptive Biasing Potential Method
fabpdef	{ABP}	string	Specifies either a PRMFile group or the name of a file containing the specification of collective variables used by the ABP method.
fabpout	_abp.out	string	Specifies the file name used for output from ABP simulations. This file contains status information and the progress of collective variables in time.
fabprst	_abp.rst	string	Specifies the name of the file containing accumulated results from ABP simulations.
fabptrj	_abp.trj	string	Specifies the name of the file containing the time evolution of accumulated ABP results.
Constrained Dynamics
fcstdef	{CST}	string	Specifies either a PRMFile group or the name of a file containing the constraint specification.
fcstout	_cst.out	string	Specifies the file name used for output from constrained dynamics simulations. This file contains status information and the progress of the calculation in time.
fcstdump	_cst.dump	string	Specifies the name of the file containing dumped data from constrained dynamics simulations.
fcstrst	_cst.rst	string	Specifies the name of the file containing results from constrained dynamics simulations. This file is used for constrained dynamics restarts.
fcsttrj	_cst.trj	string	Specifies the name of the file containing the time evolution of accumulated constrained dynamics results.
Restrained Dynamics
frstdef	{RST}	string	Specifies either a PRMFile group or the name of a file containing the specification of restraints used in restrained dynamics simulations.
frstout	_rst.out	string	Specifies the file name used for output from restrained dynamics simulations. This file contains status information and the progress of restrained collective variables in time.
frsthist	_rst.hist	string	Specifies the name of the file containing the run-time histogram of collective variables.
Metadynamics
fmtddef	{MTD}	string	Specifies either a PRMFile group or the name of a file containing the specification of metadynamics collective variables.
fmtdout	_mtd.out	string	Specifies the file name used for output from the metadynamics method. This file contains status information and the progress of collective coordinates in time.
fmtdrst	_mtd.rst	string	Specifies the name of the file containing accumulated Gaussian hills from metadynamics simulations.
fmtdtrj	_mtd.trj	string	Specifies the name of the file containing the time evolution of accumulated metadynamics results.
fmtdhills	_mtd.hills	string	Specifies the name of the file containing accumulated Gaussian hills from metadynamics simulations.
String Method
fstmdef	{STM}	string	Specifies either a PRMFile group or the name of a file containing the specification of collective variables used by the string method.
fstmout	_stm.out	string	Specifies the file name used for output from string method simulations.
Path Driving
fpdrvdef	{PDRV}	string	Specifies either a PRMFile group or the name of a file containing the path driving specification.
fpdrvout	_pdrv.out	string	Specifies the file name used for output from path driving simulations.
Collective Variable Monitoring
fmondef	{MON}	string	Specifies either a PRMFile group or the name of a file containing the specification of collective variables used during monitoring.
fmonout	_mon.out	string	Specifies the file name used for output from collective variable monitoring.
Metric Tensor Analysis
fmtadef	{MTA}	string	Specifies either a PRMFile group or the name of a file containing the specification of collective variables used by metric tensor analysis.
fmtaout	_mta.out	string	Specifies the file name used for output from metric tensor analysis.
fmtarst	_mta.rst	string	Specifies the name of the file containing accumulated results from metric tensor analysis.