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. | ||||||||||||||||||||||||||||||