Introduction

Once all seeds (local minima in the FEL) are identified, we assign all frames (with increasing free energy) to their nearest neighbor with lower free energy. By that, we guarantee that we will cut at the borders.

Execution

             
clustering density -f coordinate_file
-i network_end_node_traj.dat
-D free_energy_file
-B nearest_neighbor_file
-o output_name
-n N
-v


Parameters

Input Parameters

Parameter Description
$$\mathtt{\mbox{-}f :}$$ The name(path) of the input coordinates. The dimension should not exceed 10.
$$\mathtt{\mbox{-}i :}$$ File to initial state definition (seeds). This file is generated by $$\mathtt{network}$$ and ends with $$\mathtt{{}^*\_end\_node\_traj.dat}$$.
$$\mathtt{\mbox{-}D :}$$Filename to read the free energies from. This should be used with $$\mathtt{\mbox{-}B}$$ and a nearest neighbor file generated with the same cluster radius.
$$\mathtt{\mbox{-}B :}$$Filename to read the nearest neighbors from. This should be used with $$\mathtt{\mbox{-}D}$$ and a nearest neighbor file generated with the same clustering radius.

Output Parameters

Parameter Description
$$\mathtt{\mbox{-}o}$$This is the name of the resulting single column microstate output file.

Miscellaneous Parameters

Parameter Description
$$\mathtt{\mbox{-}n}$$The number of parallel threads to use (for SMP machines). This is ignored if CUDA is used.
$$\mathtt{\mbox{-}v}$$Verbose mode with some output.

Detailed Description

Once all seeds (local minima in the FEL) are identified, we assign all frames to their nearest neighbor with lower free energy. The frames are assigned order by their free energy from lowest to highest. This guarantees that for each frame the nearest neighbor with lower free energy is already assigned to a microstate. Further, by construction frames are never assigned to a seed which is seperated by a barrier. Hence, the states are clearly cut at the barriers as shown in following figure.