ABF:Controls: Difference between revisions

| 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]].

| fapply_abf

| on

| Determine if the collected mean force is applied as a bias.  

| 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.

| 5000

| 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.

| 5000

 

If the feimode option is equal to 1 then the following options change behavior of the linear ramp.  

| fhramp_min

| 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 the following form:

<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>

where <math>N_k</math> is the number of samples in the bin <i>k</i>.

 

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.  

| fsmoothupdate

| 5000

| 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}(\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>,

<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 an user provided factor (wfac), see [[ABF:Collective variables]].

| 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.   

| 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.