This directory contains examples of the calculations with time- and 
replica-average functions of UNRES in a canonical mode (single temperature) 
and temperature replica-exchange mode. The two first examples are those discussed in 
Shirkov, L.; Czaplewski, C.; Liwo, A. "Implementation of Replica-Averaged Restraints 
from Nuclear Magnetic Resonance Measurement with UNRES Coarse Grained Model of 
Polypeptide Chains". Molecules 2025, 30, 4354. 
https://doi.org/10.3390/molecules30224354, the third one illustrates the combination
of time- and replica-averaging, in which time-averaged quantities are averaged over
replicas. 

The directories are:

CANON : 2KW5(129-153) fragments, 4 trajectories over which the distances are
        averaged, synthetic restraints.
        Input file: 2kw5-129-153_REPAVE.inp
        PBS script file: submit.pbs

MREMD : 2LWA, temperature replica exchange, 4 temperature, 4 trajectories each,
        distance averaging over the 4 trajectories at a given temperature.
        Input file: 2LWA_AVEREP_4x4.inp
        PBS script file: submit.pbs

MREMD-TR : 2LWA, temperature replica exchange, 4 temperature, 4 trajectories each,
        distance averaging over the 4 trajectories at a given temperature, time
        averaging in each trajectory.
        Input file: 2LWA_TREPAVE_4x4.inp
        PBS script file: submit.pbs

wham : Processing the results of MREMD calculations on 2LWA with wham and cluster.
       Input file, wham : 2LWA_wham_last.inp
       PBS script file, wham : submit_wham.pbs
       Input file, cluster : 2LWA_clust.inp
       PBS script file, cluster : submit_cluster.pbs

wham-TR : As above but for MREMD-TR.

Please note that the batch script files must be edited to point to the location
of unres, wham, and cluster executables and the UNRES parameter file.

The OUTPUT subdirectory of each of the above mentioned directories contains
sample results. Please note that because molecular dynamics starts from
randomly-generated structures and velocities, these results might differ from
those obtained with other hardware architectures.

