Merge branch 'prerelease-3.2.1' into czarek

[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
+