ABF:Controls: Difference between revisions
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| 0 | | 0 | ||
| [[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 (four points)<br/> 2 - less accurate | | 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 implementation is used (two points)<br/>If the method is enabled then at least one collective variable must be provided in the {ABF} group. The collective variable specification is described in [[ABF:Collective variables]]. | ||
|- style="vertical-align: top;" | |- style="vertical-align: top;" | ||
| | | fapply_abf | ||
| | | on | ||
| [[Control key types|logical]] | | [[Control key types|logical]] | ||
| | | Determine if the collected mean force is applied as a bias. | ||
|- style="vertical-align: top; background-color: #f6f6f6;" | |- style="vertical-align: top; background-color: #f6f6f6;" | ||
| feimode | | feimode | ||
| 1 | | 1 | ||
| [[Control key types|integer]] | | [[Control key types|integer]] | ||
| 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 | | 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 below. | ||
|- style="vertical-align: top;" | |- style="vertical-align: top;" | ||
| fsample | | fsample | ||
| 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, then warning is raised | | 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 and the simulation continues. | ||
|- style="vertical-align: top;" | |- style="vertical-align: top;" | ||
| frstupdate | | frstupdate | ||
| Line 46: | Line 46: | ||
| 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;" | |- style="vertical-align: top;" | ||
| fmask | |||
| off | |||
| [[Control key types|logical]] | |||
| Disable/Enable ABF force weights (mask). The name of file with the ABF weights is provided in the [[General setup|[files]]] section. This option has only sense if more than one collective variable is requested and some regions in such CV space should not be sampled. | |||
|- style="vertical-align: top; background-color: #f6f6f6;" | |||
| fenthalpy | | fenthalpy | ||
| off | | off | ||
| [[Control key types|logical]] | | [[Control key types|logical]] | ||
| If enabled, data for enthalpy calculation are collected. | | If enabled, data for enthalpy calculation are collected. | ||
|- style="vertical-align: top | |- style="vertical-align: top;" | ||
| entropy | | entropy | ||
| off | | off | ||
| [[Control key types|logical]] | | [[Control key types|logical]] | ||
| If enabled, data for entropy (-TdS) calculation are collected. | | If enabled, data for entropy (-TdS) calculation are collected. | ||
|- style="vertical-align: top;" | |- style="vertical-align: top; background-color: #f6f6f6;" | ||
| fepotoffset | | fepotoffset | ||
| 0.0 | | 0.0 | ||
| [[Control key types|real]] | | [[Control key types|real]] | ||
| A constant, which is added to the potential energy (affect the enthalpy calculation). | | A constant, which is added to the potential energy (affect the enthalpy calculation). | ||
|- style="vertical-align: top | |- style="vertical-align: top;" | ||
| fekinoffset | | fekinoffset | ||
| 0.0 | | 0.0 | ||
| Line 66: | Line 71: | ||
| A constant, which is added to the kinetic energy (affect the entropy calculation). | | 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 | ===Linear ramp=== | ||
If the feimode option is equal to 1 then the following options change behavior of the linear ramp. | |||
{| style="width: 100%;" | {| style="width: 100%;" | ||
| style="width: 10em;" | '''Key''' | | style="width: 10em;" | '''Key''' | ||
| Line 77: | Line 83: | ||
| 200 | | 200 | ||
| [[Control key types|integer]] | | [[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 | | 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 applied. | ||
|- style="vertical-align: top;" | |- style="vertical-align: top;" | ||
| fhramp_max | | fhramp_max | ||
| 500 | | 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 | | 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 applied fully otherwise it is scaled down by the linear ramp. | ||
|} | |} | ||
The linear ramp has following form: | The linear ramp has the following form: | ||
<center><math>\bold F_{ | <center><math>\bold F_{applied} = \frac{N_k - fhramp\_min}{fhramp\_max-fhramp\_min}\bold F_{estimated}</math>, if <math>N_k < fhramp\_max</math>,</center> | ||
otherwise the full force is applied: | |||
If the feimode option is equal to 2 then following option changes | <center><math>\bold F_{applied} = \bold F_{estimated}</math>,</center> | ||
where <math>N_k</math> is the number of samples in the bin <i>k</i>. | |||
===Gaussian kernel smoothing=== | |||
If the feimode option is equal to 2 then the following option changes behavior 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 97: | Line 107: | ||
| 5000 | | 5000 | ||
| [[Control key types|integer]] | | [[Control key types|integer]] | ||
| The | | The value determines how often (in MD steps) the smoothed mean forces are updated. | ||
|} | |} | ||
The relationships between the sampled instantaneous collective and smoothed forces is given: | |||
<center><math>\bold F_{aplied}(\mathbf{\xi}_i) = \frac{ \sum\limits_{j=1}^{N_{bins}} K(\mathbf{\xi}_i,\mathbf{\xi}_j)\bold F_{estimated}(\mathbf{\xi}_j)} {\sum\limits_{j=1}^{N_{bins}} K(\mathbf{\xi}_i,\mathbf{\xi}_j) }</math></center>, | |||
with the Gaussian smoothing kernel defined as: | |||
<center><math>K(\bold\xi_i,\bold\xi_j) = exp\left( - \frac {1}{2} \sum\limits_{k=1}^{N_{CVS}} \frac { (\xi_{i,k} - \xi_{j,k})^2} { w_{k}^2 h_{k}^2 } \right)</math></center>, | |||
where <math>h_{k}^2</math> is a bin width and <math>w_{k}^2</math> is user provided factor (wfac), see [[ABF:Collective variables]]. | |||
==[abf-walker]== | ==[abf-walker]== | ||