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[unres.git] / examples / README.txt

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-This directory contains examples of calculactions with UNRES, run on small
-systems. The following directories contain calculations of different
-categories:
-
-MD - molecular-dynamics-related calculations
-
-  microcanonical - microcanonical calculations
-
-      VTS - calculations with variable time step 
-          ff_1l2y - 1E0L1L2Y force field
-          ff_gab - 1GAB force field
-
-      RESPA - calculations with the AMTS algorithm
-          ff_1l2y - 1E0L1L2Y force field
-          ff_gab - 1GAB force field
-
-  Berendsen - calculations with Berendsen's thermostat
-          ff_1l2y - 1E0L1L2Y force field
-          ff_gab - 1GAB force field
-          
-  Nose_Hoover - calculations with Nose-Hoover thermostat
-          ff_1l2y - 1E0L1L2Y force field
-          ff_gab - 1GAB force field
-
-  Langevin - Langevin dynamics calculations
-          ff_1l2y - 1E0L1L2Y force field
-          ff_gab - 1GAB force field
-
-REMD - calculations with replica exchange molecular dynamics
- 
-  Berendsen - calculations with Berendsen's thermostat
-          ff_1l2y - 1E0L1L2Y force field
-          ff_gab - 1GAB force field
-          
-  Nose_Hoover - calculations with Nose-Hoover thermostat
-          ff_1l2y - 1E0L1L2Y force field
-          ff_gab - 1GAB force field
-
-  Langevin - Langevin dynamics calculations
-          ff_1l2y - 1E0L1L2Y force field
-          ff_gab - 1GAB force field
-
-  with_constraints - calculations with distance restraints
-
-      Berendsen - Berendsen calculations (the only examples for restrained
-                  REMD)
-
-          ff_1l2y - 1E0L1L2Y force field
-          ff_gab - 1GAB force field
-
-MREMD - multiplexed replica-exchange calculations
-
-          ff_1l2y - 1E0L1L2Y force field
-          ff_gab - 1GAB force field
-
-
-CSA - conformational space annealing calculations
-
-  4P       - 4P force field
-  1E0LL2Y  - 1E0LL2Y force field
-  GAB      - 1GAB force field
-
-MINIM - energy minimization calculations
-
-MULTICHAIN - sample runs on oligomeric proteins
-
-Each bottom directory contains the respective batch and C-shell scripts, 
-input file, and the output directory that contains the results of sample
-calculations, which can be checked against the results of user's 
-calculations
-