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Adding partially finished OPTIM stationary points to a PATHSAMPLE…
https://wikis.ch.cam.ac.uk/ro-walesdocs/wiki/index.php/Adding_partially_finished_OPTIM_stationary_points_to_a_PATHSAMPLE_databaseNavigation. Tools. This page was last edited on 10 May 2019, at 18:24. -
Generating parameters using AMBER's built in General Forcefield…
https://wikis.ch.cam.ac.uk/ro-walesdocs/wiki/index.php/Generating_parameters_using_AMBER%27s_built_in_General_Forcefield_(gaff)Navigation. Tools. This page was last edited on 13 May 2019, at 10:24. -
Calculating rate constants (GT and fastest path) - Docswiki
https://wikis.ch.cam.ac.uk/ro-walesdocs/wiki/index.php/Calculating_rate_constants_(GT_and_fastest_path)2100556 Dijkstra> MFPT for fastest path: A<-B value= 0.7030943368E25 B<-A value= 0.2425804971E-08 Dijkstra> rates without conditional probability: A<-B value= 0.1422284248E-24 B<-A value= ... 412234294.2 Dijkstra> rates with conditional probability: A<-B -
Calculating binding free energy using the FSA method - Docswiki
https://wikis.ch.cam.ac.uk/ro-walesdocs/wiki/index.php/Calculating_binding_free_energy_using_the_FSA_methodPAC A 317 17.578 25.580 63.751 1.00 15.05 C ATOM 2564 C1' PAC A 317 17.351 24.336 62.935 1.00 22.49 C ... 00 15.05 H ATOM 0 H2' PAC A 317 19.077 24.466 61.823 1.00 24.42 H. -
Finding an initial path with OPTIM and starting up PATHSAMPLE…
https://wikis.ch.cam.ac.uk/ro-walesdocs/wiki/index.php/Finding_an_initial_path_with_OPTIM_and_starting_up_PATHSAMPLE_(CHARMM)144.0096582 5.4996 -149.5092547 24.935 17.263 1.969 24.372 18 -149.5092547 0.11279E-01 -149.4979756 3.8322 -153.3301944 6.223 5.891
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