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 |
| Collective Variables | |||
| 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 | |
| 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. |
| 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. |
| 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. |
| MTC Method | |||
| fmtcdef | {MTC} | string | |
| fmtcout | _mtc.out | string | |
| fmtcrst | _mtc.rst | 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. |
| Path Driving | |||
| fpdrvdef | {PDRV} | string | |
| fpdrvout | _pdrv.out | string | |