gmxcoco.wcfg

#--------------------------------------------------General------------------------------------------------------
num_iterations             = 2                                # Number of iterations of Simulation-Analysis
start_iter                 = 0                                # Iteration number with which to start
num_CUs   	           = 2                               # Number of tasks or Compute Units
nsave		           = 1	                              # Iterations after which output is transferred to local machine

#--------------------------------------------------Simulation--------------------------------------------------
num_cores_per_sim_cu      = 1                                 # Number of cores per Simulation Compute Units
initial_crd_file          = './inp_files/helix.gro'           # Entire path to Coordinates file - Do not use $HOME or the likes
md_input_file             = './inp_files/grompp-verlet.mdp'   # Entire path to MD Input file - Do not use $HOME or the likes
top_file                  = './inp_files/topol.top'           # Entire path to Topology file - Do not use $HOME or the likes
#ndx_file                  = './inp_files/index.ndx'          # Entire path to Index file - Do not use $HOME or the likes
itp_file                  = './inp_files/posre.itp'           # Entire path to ITP file - Do not use $HOME or the likes
restr_file                = './inp_files/helix.gro'           # Entire path to initial structure from which we will start the position restraints simulations
eminrestr_md              = './inp_files/grompp_after_coco-em1.mdp'
eeqrestr_md               = './inp_files/grompp_after_coco-em2.mdp'

#---------------------------------------------------Analysis-------------------------------------------------------------
grid                      = '30'                              # Number of points along each dimension of the CoCo histogram
dims                      = '3'                               # The number of projections to consider from the input pcz file
sel                       = 'protein'                         # Select the part of the system to be considered for coco analysis
output                    = 'coco_out.gro'                    # Specify base name for the output files where the extension will indicate the format of the output

misc_loc = './misc_files'