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force_field_parameters
force_field_parameters
 
 
utils
utils
 
 
README.md
README.md
 
 
load-with-stride.tcl
load-with-stride.tcl
 
 
tcl_for_mutating.tcl
tcl_for_mutating.tcl
 
 
tk_d436_r445.tcl
tk_d436_r445.tcl
 
 
tk_e428_r445.tcl
tk_e428_r445.tcl
 
 
tk_mutation_on_GltPh.tcl
tk_mutation_on_GltPh.tcl
 
 
tk_mv2.tcl
tk_mv2.tcl
 
 
tk_na2_d421.tcl
tk_na2_d421.tcl
 
 
tk_na2_d79.tcl
tk_na2_d79.tcl
 
 
tk_na2_e428.tcl
tk_na2_e428.tcl
 
 
tk_na2_na1.tcl
tk_na2_na1.tcl
 
 
tk_na2_water_coord.tcl
tk_na2_water_coord.tcl
 
 
tk_r60_d436.tcl
tk_r60_d436.tcl
 
 
tk_r60_e428.tcl
tk_r60_e428.tcl
 
 
tk_r60_e446.tcl
tk_r60_e446.tcl
 
 
tk_r60_y335.tcl
tk_r60_y335.tcl
 
 
tk_rename_segments.tcl
tk_rename_segments.tcl
 
 
tk_volmap.py
tk_volmap.py
 
 
tk_y335_e428.tcl
tk_y335_e428.tcl
 
 

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Analysing Molecular Dynamics Simulations

Tcl scripts for calculating tICA parameters in this paper:

A Markov State-based Quantitative Kinetic Model of Sodium Release from the Dopamine Transporter

https://www.nature.com/articles/srep40076

  • There are also some other Tcl scripts for preparing MD simulations using VMD

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Running and analyzing scripts for MD simulations

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