ABF:Controls: Difference between revisions
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| [[Control key types|integer]] | | [[Control key types|integer]] | ||
| The mode of the ABF method:<br/>0 - the method is disabled<br/> 1 - the standard ABF implementation is used<br/> 2 - less accurate implemetation is used<br/>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]]. | | The mode of the ABF method:<br/>0 - the method is disabled<br/> 1 - the standard ABF implementation is used (four points)<br/> 2 - less accurate implemetation is used (two points)<br/>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]]. | ||
|- style="vertical-align: top;" | |- style="vertical-align: top;" | ||
| fmask | | fmask | ||
| Line 24: | Line 24: | ||
| 1 | | 1 | ||
| [[Control key types|integer]] | | [[Control key types|integer]] | ||
| The extrapolation/interpolation mode for ABF forces:<br/> | | The extrapolation/interpolation mode for ABF forces:<br/>0 - disabled<br/>1 - linear ramp with bottom limit<br/>2 - Gaussian kernel smoothing<br/>This option triggers further setup, which is optional and described in details below. | ||
|- style="vertical-align: top;" | |- style="vertical-align: top;" | ||
| fsample | | fsample | ||
| | | 5000 | ||
| [[Control key types|integer]] | | [[Control key types|integer]] | ||
| Every <i>fsample</i> 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 [[General setup|[files]]] section. | | Every <i>fsample</i> 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 [[General setup|[files]]] section. | ||
| Line 34: | Line 34: | ||
| off | | off | ||
| [[Control key types|logical]] | | [[Control key types|logical]] | ||
| Disable/Enable restarting the ABF simulation from the previous run. The name of the restart file is provided in the [[General setup|[files]]] section. If the restart is enabled but no restart file exists | | Disable/Enable restarting the ABF simulation from the previous run. The name of the restart file is provided in the [[General setup|[files]]] section. If the restart is enabled but no restart file exists, then warning is raised but the simulation continues. | ||
|- style="vertical-align: top;" | |- style="vertical-align: top;" | ||
| frstupdate | | frstupdate | ||
| | | 5000 | ||
| [[Control key types|integer]] | | [[Control key types|integer]] | ||
| Every <i>frstupdate</i> 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 [[General setup|[files]]] section. | | Every <i>frstupdate</i> 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 [[General setup|[files]]] section. | ||
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| [[Control key types|integer]] | | [[Control key types|integer]] | ||
| Every <i>ftrjsample</i> 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 [[General setup|[files]]] section. Zero interval disables the ABF trajectory writing. | | Every <i>ftrjsample</i> 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 [[General setup|[files]]] section. Zero interval disables the ABF trajectory writing. | ||
|- style="vertical-align: top;" | |||
| fenthalpy | |||
| off | |||
| [[Control key types|logical]] | |||
| If enabled, data for enthalpy calculation are collected. | |||
|- style="vertical-align: top; background-color: #f6f6f6;" | |||
| entropy | |||
| off | |||
| [[Control key types|logical]] | |||
| If enabled, data for entropy (-TdS) calculation are collected. | |||
|- style="vertical-align: top;" | |||
| fepotoffset | |||
| 0.0 | |||
| [[Control key types|real]] | |||
| A constant, which is added to the potential energy (affect the enthalpy calculation). | |||
|- style="vertical-align: top; background-color: #f6f6f6;" | |||
| fekinoffset | |||
| 0.0 | |||
| [[Control key types|real]] | |||
| A constant, which is added to the kinetic energy (affect the entropy calculation). | |||
|} | |} | ||
---- | ---- | ||
If the feimode option is equal to 1 then following | If the feimode option is equal to 1 then following options change behaviour of the linear ramp. | ||
{| style="width: 100%;" | {| style="width: 100%;" | ||
| style="width: 10em;" | '''Key''' | | style="width: 10em;" | '''Key''' | ||
| Line 54: | Line 74: | ||
| '''Description''' | | '''Description''' | ||
|- style="vertical-align: top; background-color: #f6f6f6;" | |- style="vertical-align: top; background-color: #f6f6f6;" | ||
| | | fhramp_min | ||
| | | 200 | ||
| [[Control key types|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. | |||
|- style="vertical-align: top;" | |||
| fhramp_max | |||
| 500 | |||
| [[Control key types|integer]] | | [[Control key types|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. | | 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: | The linear ramp has following form: | ||
<center><math>\bold F_{aplied} = \frac{N_k}{fhramp}\bold F_{estimated}</math>, where N<sub>k</sub> is the number samples in bin <i>k</i></center> | <center><math>\bold F_{aplied} = \frac{N_k - fhramp\_min}{fhramp\_max-fhramp\_min}\bold F_{estimated}</math>, where N<sub>k</sub> is the number samples in bin <i>k</i></center> | ||
---- | ---- | ||
If the feimode option is equal to 2 then following option changes behaviour of the | 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. | ||
{| style="width: 100%;" | {| style="width: 100%;" | ||
| style="width: 10em;" | '''Key''' | | style="width: 10em;" | '''Key''' | ||
| Line 69: | Line 94: | ||
| '''Description''' | | '''Description''' | ||
|- style="vertical-align: top; background-color: #f6f6f6;" | |- style="vertical-align: top; background-color: #f6f6f6;" | ||
| | | fsmoothupdate | ||
| | | 5000 | ||
| [[Control key types|integer]] | | [[Control key types|integer]] | ||
| | | The walue determines how often (in MD steps) the smoothed mean forces are updated. | ||
|} | |} | ||
==[abf-walker]== | ==[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]]. | |||
{| style="width: 100%;" | {| style="width: 100%;" | ||
| style="width: 10em;" | '''Key''' | | style="width: 10em;" | '''Key''' | ||