This directory contains examples of the calculations with replica-average
function of UNRES in a canonical mode (single temperature) and temperature
replica-exchange mode. The examples are those discussed in 
L. Shirkov, C. Czaplewski, A. Liwo, "Implementation of Replica-Averaged 
Restraints from Nuclear Magnetic Resonance Measurement with UNRES Coarse
Grained Model of Polypeptide Chains", Molecules, in review.

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

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

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.


