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<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
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| 1
| 1
| [[Control key types|integer]]
| [[Control key types|integer]]
| The extrapolation/interpolation mode for ABF forces:<br/>1 - simple linear ramp<br/>2 - linear ramp with bottom limit<br/>This option triggers further setup, which is optional and described in details below.
| 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
| 500
| 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.  
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| 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 only 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 but the simulation continues.
|- style="vertical-align: top;"
|- style="vertical-align: top;"
| frstupdate
| frstupdate
| 1000
| 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 option changes behaviour of the linear ramp.  
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'''  
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| '''Description'''
| '''Description'''
|- style="vertical-align: top; background-color: #f6f6f6;"
|- style="vertical-align: top; background-color: #f6f6f6;"
| fhramp
| fhramp_min
| 100
| 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 linear ramp.  
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'''  
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| '''Description'''
| '''Description'''
|- style="vertical-align: top; background-color: #f6f6f6;"
|- style="vertical-align: top; background-color: #f6f6f6;"
| fhramp_min
| fsmoothupdate
| 200
| 5000
| [[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.  
| The walue determines how often (in MD steps) the smoothed mean forces are updated.
|}
|}
The linear ramp has following form:
<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>


The optional section [abf-walker] provides information about access to the MWA server. The MWA extension is described in detail in [[ABF:Multiple walkers approach]].


==[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'''  

Revision as of 15:21, 21 July 2021

Navigation: Documentation / Methods / Adaptive Biasing Force Method / ABF:Controls

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:

, where Nk is the number samples in bin k

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.
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