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* [[MTD:Post-processing]]
* [[MTD:Post-processing]]
* [[MTD:Multiple walkers approach]]
* [[MTD:Multiple walkers approach]]
* [[MTD:Examples]]
* [[MTD:Utilities]]
* [[MTD:Utilities]]
* [[MTD:Examples]]


==Description==
==Description==
===Theory===
===Free Energy from Metadynamics Simulations===
 
Metadynamics introduces a history-dependent potential, which is composed of Gaussian functions added in regular intervals. This potential is employed as a bias in molecular dynamics simulation to suppress visiting already sampled regions.  
 
== Single mode ==
Single mode of metadynamics follows same common rules as all other PMFLib methods (same definition of CVs, same syntax). It has peculiar sections
 
SubSection [mtd] in {PMFLIB} section with general metadynamics setup common for whole run (example follows):
  [mtd]
  fmode  1                                                                                                                                 
  fserverkey server.key                                                                                                                     
  fsample 100                                                                                                                               
  fheight 0.01                                                                                                                             
  frestart on
 
Section {MTD} defining particular configuration for each CV (example follows):
  {MTD}                                                                                                                                     
  [CV]                                                                                                                                     
  name d1                                                                                                                                   
  min_value    5.0                                                                                                                         
  max_value  30.0                                                                                                                         
  nbins      100                                                                                                                           
  width        0.5
 
== Multiple walker mode ==
Server has to be run and available during all calculation (submit to apropriate queue). Any number of clients that connect to server with results.
 
; Server
'''mtd-admin''' - Admin program, is able to connect to server and submit commands to server. Available commands are:
  info    = prints information about registered clients
  flush    = saves accumulated MTD data on server side
  get      = gets accumulated MTD data and saves them locally
  shutdown = stops server execution
  errors  = prints errors from server stack
See mtd-admin help for more info.
 


'''mtd-server''' - is multiple walker metadynamics server program. It requires input file with sections and keywords mentioned below:
<center><math>V_{MTD}(\boldsymbol \xi) = \sum_{t=1}^{T_{MTD}} h_t exp \left( - \frac{1}{2} \frac{(\boldsymbol \xi - \boldsymbol \xi_t)^2}{\boldsymbol \sigma} \right) </math> ... (8)</center>


Section [server]
As a result, the system evolves by free diffusions alongside biased collective variables.  Moreover, the history-dependent potential converges to the negative value of the free energy in a limit of infinitesimally long metadynamics simulation.
:Server key file name  (serverkey)              = server.key
:Do not automatically shutdown (donotshutdown) =  false                (default)
:Listening queue length (maxqueuelen)          =    30                (default)
:Max number of worker threads (maxthreads)      =      5                (default)




Section [watcher]
:Watcher service is enabled (enabled)          =  true                (default)
:Flush dead clients interval (deadinterval) [s] =  3600                (default)
:Flush error stack interval (errorinterval) [s] =    30                (default)
:Error log file (logname)                      = errors.log            (default)


Section [files]
The application of the history dependent potential thus leads to the modified equations of motions:
:Input history potential (input)  = none                              (default)
:Output history potential (output) = _mtdserver.rst                    (default)


<center><math>m_{i}  \frac { d^2 \bold r_i }{dt^2} = \bold F_{pot,i}(\bold r_i) - \bold F_{bias,i}(\bold r_i) = - \frac{\partial V(\bold R)} {\partial \bold r_i} - \frac{\partial G(\boldsymbol \xi)}{\partial \boldsymbol \xi} \frac{\partial \boldsymbol \xi}{\partial \bold r_i}</math> ... (8)</center>


; Client
where <math>m_i</math> is mass of atom i, <math>\bold r_i</math> is atom position, and <math>t</math> is time.
Client setup is analogous to one in single mode, it contains section [mtd] and extra definition section [mtd-walker] with keyword fserverkey and server key file has to be accesible to client (via it can connect to client):


  [mtd-walker]
Since the biasing force is not known prior to the simulation, it is calculated during the simulation and adaptively applied. To accelerate sampling, the biasing force is applied even if an inadequate number of samples is collected in a bin. In this case, the biasing force is scaled in the early stages to avoid artifacts from applications of overestimated biasing forces. The biasing force can also be smoothed to decrease noise in collected data. For further details, see feimode in [[ABF:Controls]].
  fserverkey server.key

Revision as of 16:00, 22 July 2021

Navigation: Documentation / Methods / Metadynamics

Contents

Description

Free Energy from Metadynamics Simulations

Metadynamics introduces a history-dependent potential, which is composed of Gaussian functions added in regular intervals. This potential is employed as a bias in molecular dynamics simulation to suppress visiting already sampled regions.

... (8)

As a result, the system evolves by free diffusions alongside biased collective variables. Moreover, the history-dependent potential converges to the negative value of the free energy in a limit of infinitesimally long metadynamics simulation.


The application of the history dependent potential thus leads to the modified equations of motions:

... (8)

where is mass of atom i, is atom position, and is time.

Since the biasing force is not known prior to the simulation, it is calculated during the simulation and adaptively applied. To accelerate sampling, the biasing force is applied even if an inadequate number of samples is collected in a bin. In this case, the biasing force is scaled in the early stages to avoid artifacts from applications of overestimated biasing forces. The biasing force can also be smoothed to decrease noise in collected data. For further details, see feimode in ABF:Controls.

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