ABF:Controls: Difference between revisions
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| 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;" | ||
| | | fapply_mask | ||
| off | | off | ||
| [[Control key types|logical]] | | [[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. | | Disable/Enable ABF force weights (mask). The name of file with the ABF weights is provided in the [[General setup|[files]]] section. The ABF mask is suitable for difficult free energy surfaces containing high energy regions, which is not necessary/appropriate to sample. | ||
|- style="vertical-align: top; background-color: #f6f6f6;" | |- style="vertical-align: top; background-color: #f6f6f6;" | ||
| fenthalpy | | fenthalpy | ||
| Line 56: | Line 56: | ||
| If enabled, data for enthalpy calculation are collected. | | If enabled, data for enthalpy calculation are collected. | ||
|- style="vertical-align: top;" | |- style="vertical-align: top;" | ||
| | | fentropy | ||
| off | | off | ||
| [[Control key types|logical]] | | [[Control key types|logical]] | ||
| Line 81: | Line 81: | ||
|- style="vertical-align: top; background-color: #f6f6f6;" | |- style="vertical-align: top; background-color: #f6f6f6;" | ||
| fhramp_min | | fhramp_min | ||
| | | 100 | ||
| [[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 applied. | | 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 | ||
| | | 200 | ||
| [[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 applied 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 applied fully otherwise it is scaled down by the linear ramp. | ||
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|} | |} | ||
The relationships between the sampled instantaneous collective and smoothed forces is given: | The relationships between the sampled instantaneous collective and smoothed forces is given: | ||
<center><math>\bold F_{aplied}(\ | <center><math>\bold F_{aplied}(\boldsymbol \xi_i) = \frac{ \sum\limits_{j=1}^{N_{bins}} K(\boldsymbol \xi_i,\boldsymbol \xi_j)\bold F_{estimated}(\boldsymbol \xi_j)} {\sum\limits_{j=1}^{N_{bins}} K(\boldsymbol \xi_i,\boldsymbol \xi_j) }</math></center>, | ||
with the Gaussian smoothing kernel defined as: | with the Gaussian smoothing kernel defined as: | ||
<center><math>K(\ | <center><math>K(\boldsymbol \xi_i,\boldsymbol \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]]. | where <math>h_{k}^2</math> is a bin width and <math>w_{k}^2</math> is an user provided factor (wfac), see [[ABF:Collective variables]]. | ||
==[abf-walker]== | ==[abf-walker]== | ||