General setup
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The general setup of PMFLib can be controlled through the following sections in the {PMFLIB} group. They control the behaviour of the PMFLib core ([control]), define the units used for input data specification ([units]), and the names of input and output files ([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: au, a.u., g/mol, amu |
| time | fs | string | Unit of time. Allowed values are: au, a.u., fs, ps |
| length | A | string | Unit of length. Allowed values are: au, a.u., A, pm, nm |
| angle | deg | string | Unit of angle. Allowed values are: rad, deg |
| energy | kcal/mol | string | Unit of energy. Allowed values are: au, a.u., eV, kcal/mol, kJ/mol |
| temperature | K | string | Unit of temperature. Allowed values are: K |
| pressure | Pa | string | 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 | |
| fpathsdef | {PATHS} | string | |
| 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. |
| fabfmask | _abf.mask | string | It defines the name of the file that contains ABF force weights. |
| fabfout | _abf.out | string | It defines the 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 the file with accumulated results from ABF simulations. |
| fabftrj | _abf.trj | string | It defines the name of the file containing the time evolution of accumulated ABF results. |
| Adaptive Biasing Potential Method | |||
| fabpdef | {ABP} | string | |
| fabpout | _abp.out | string | |
| fabprst | _abp.rst | string | |
| fabptrj | _abp.trj | string | |
| Constrained Dynamics | |||
| fcstdef | {CST} | string | It defines either a PRMFile group or a file name containing the specification of constraints. |
| fcstout | _cst.out | string | It defines the file name used as output from constrained dynamics simulations. This file contains status information and the progress of the calculation in time. |
| fcstdump | _cst.dump | string | |
| fcstrst | _cst.rst | string | It defines the name of the file with results from the constrained dynamics simulation. This file is used for constrained dynamics calculation restarts. |
| fcstctr | string | ||
| fcsttrj | _cst.trj | string | |
| Restrained Dynamics | |||
| frstdef | {RST} | string | It defines either a PRMFile group or a file name containing the specification of restraints used in restrained dynamics simulations. |
| frstout | _rst.out | string | It defines the file name used as output from restrained dynamics simulations. This file contains status information and the progress of restrained collective variables in time. |
| frsthist | _rst.hist | string | It defines the name of the file containing the run-time histogram of collective variables. |
| 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 the 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 the file containing accumulated Gaussian hills from metadynamics simulations. |
| fmtdtrj | _mtd.trj | string | |
| fmtdhills | _mtd.hills | string | It defines the name of the file containing accumulated Gaussian hills from metadynamics simulations. |
| 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 the file name used as output from string method simulations. |
| Path Driving | |||
| fpdrvdef | {PDRV} | string | |
| fpdrvout | _pdrv.out | string | |
| 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 the file name used as output from collective variable monitoring. |
| Metric Tensor Correction | |||
| fmtcdef | {MTC} | string | |
| fmtcout | _mtc.out | string | |
| fmtcrst | _mtc.rst | string | |