1 This directory contains examples of calculactions with UNRES, run on small
2 systems. The following directories contain calculations of different
5 MD - molecular-dynamics-related calculations
7 microcanonical - microcanonical calculations
9 VTS - calculations with variable time step
10 ff_1l2y - 1E0L1L2Y force field
11 ff_gab - 1GAB force field
13 RESPA - calculations with the AMTS algorithm
14 ff_1l2y - 1E0L1L2Y force field
15 ff_gab - 1GAB force field
17 Berendsen - calculations with Berendsen's thermostat
18 ff_1l2y - 1E0L1L2Y force field
19 ff_gab - 1GAB force field
21 Nose_Hoover - calculations with Nose-Hoover thermostat
22 ff_1l2y - 1E0L1L2Y force field
23 ff_gab - 1GAB force field
25 Langevin - Langevin dynamics calculations
26 ff_1l2y - 1E0L1L2Y force field
27 ff_gab - 1GAB force field
29 REMD - calculations with replica exchange molecular dynamics
31 Berendsen - calculations with Berendsen's thermostat
32 ff_1l2y - 1E0L1L2Y force field
33 ff_gab - 1GAB force field
35 Nose_Hoover - calculations with Nose-Hoover thermostat
36 ff_1l2y - 1E0L1L2Y force field
37 ff_gab - 1GAB force field
39 Langevin - Langevin dynamics calculations
40 ff_1l2y - 1E0L1L2Y force field
41 ff_gab - 1GAB force field
43 with_constraints - calculations with distance restraints
45 Berendsen - Berendsen calculations (the only examples for restrained
48 ff_1l2y - 1E0L1L2Y force field
49 ff_gab - 1GAB force field
51 MREMD - multiplexed replica-exchange calculations
53 ff_1l2y - 1E0L1L2Y force field
54 ff_gab - 1GAB force field
57 CSA - conformational space annealing calculations
60 1E0LL2Y - 1E0LL2Y force field
61 GAB - 1GAB force field
63 MINIM - energy minimization calculations
65 MULTICHAIN - sample runs on oligomeric proteins
67 Each bottom directory contains the respective batch and C-shell scripts,
68 input file, and the output directory that contains the results of sample
69 calculations, which can be checked against the results of user's