ABF:Controls
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The behavior of the ABF method is controlled by the setup provided in the [abf] and eventually [abf-walker] sections. Both sections belong to the {PMFLIB} group.
[abf]
| Key | Default value | Type | Description |
| fmode | 0 | integer | The mode of the ABF method: 0 - the method is disabled 1 - the standard ABF implementation is used (four points) 2 - less accurate implemetation is used (two points) If the method is enabled then at least one collective variable should be provided in the {ABF} group. The collective variable specification is described in ABF:Collective variables. |
| fmask | off | logical | Disable/Enable ABF force weights (mask). The name of file with the ABF weights is provided in the [files] section. This option has only sense if more than one collective variable is requested and some region in such CV space should not be sampled. |
| feimode | 1 | integer | The extrapolation/interpolation mode for ABF forces: 0 - disabled 1 - linear ramp with bottom limit 2 - Gaussian kernel smoothing This option triggers further setup, which is optional and described in details below. |
| fsample | 5000 | integer | Every fsample MD steps, the actual information about collective variable values will be printed to the ABF output file. The name of the output file is provided in the [files] section. |
| frestart | off | logical | Disable/Enable restarting the ABF simulation from the previous run. The name of the restart file is provided in the [files] section. If the restart is enabled but no restart file exists, then warning is raised but the simulation continues. |
| frstupdate | 5000 | integer | Every frstupdate MD steps, the actual ABF force and other data will be printed to the ABF restart file. The name of the restart file is provided in the [files] section. |
| ftrjsample | 0 | integer | Every ftrjsample MD steps, the actual ABF acumulator and other data will be printed to the ABF trajectory file. The name of the trajectory file is provided in the [files] section. Zero interval disables the ABF trajectory writing. |
| fenthalpy | off | logical | If enabled, data for enthalpy calculation are collected. |
| entropy | off | logical | If enabled, data for entropy (-TdS) calculation are collected. |
| fepotoffset | 0.0 | real | A constant, which is added to the potential energy (affect the enthalpy calculation). |
| fekinoffset | 0.0 | real | A constant, which is added to the kinetic energy (affect the entropy calculation). |
If the feimode option is equal to 1 then following options change behaviour of the linear ramp.
| Key | Default value | Type | Description |
| fhramp_min | 200 | integer | Bottom limit for number of samples in a bin. If the actual number of samples in a bin is lower than this number no ABF force is aplied. |
| fhramp_max | 500 | integer | Top limit for number of samples in a bin. If the actual number of samples in a bin is higher than this number then estimated ABF force is aplied fully otherwise it is scaled down by the linear ramp. |
The linear ramp has following form:
If the feimode option is equal to 2 then following option changes behaviour of the Gaussian kernel smoothing. This filter requires an additional parameter (wfac) specified for each CV.
| Key | Default value | Type | Description |
| fsmoothupdate | 5000 | integer | The walue determines how often (in MD steps) the smoothed mean forces are updated. |
[abf-walker]
The optional section [abf-walker] provides information about access to the MWA server. The MWA extension is described in ABF:Multiple walkers approach.
| Key | Default value | Type | Description |
| fserverkey | string | The name of a file with a server key. The server key contains information about the server name, the port number, and the server password. The file is generated by the mwa-server utility when the MWA server is started. | |
| fserverupdate | 20000 | integer | The number of MD steps between exchanges of data with the MWA server. Since data are exchanged in a connect/send/receive/disconnect mode, exchanges should not occur too often. |
| fabortonmwaerr | on | logical | Should the running of a walker (client) abort when MWA server communication failure occurs? |
| fconrepeats | 0 | integer | The number of consecutive failed exchanges with the server that will lead to premature client termination. The zero means that no failures are allowed and the client is terminated at the first failed exchange. |