**** Set paths, input and output filenames, and output data formats
<<<< filenames
** Directory where output data are saved
path = /data/bhandariyr/cafemol/ring/run1/inp1/out1
** Output file names up to the suffix
filename = monomer
** Types of output files
OUTPUT pdb psf dcd rst
** Directory where the parameter files are prepared
path_para = /data/PNAI/yuba/software/cafemol_mod/para/
** Directory where the native (reference) structures are prepared
path_pdb = /data/bhandariyr/cafemol/ring/run1/pdb
** Directory where the initial structures are prepared
path_ini = /data/bhandariyr/cafemol/ring/run1/pdb
** Directory where the native (reference) information are prepared
path_natinfo = /data/bhandariyr/cafemol/ring/run1/ninfo
>>>>

**** Set the overall job
<<<< job_cntl
** Constant temperature simulation 2, simulated annealing 3
i_run_mode = 2
** Langevin dynamics
i_simulate_type = 1
** Configuration given in the input with the CafeMol (CG) style
i_initial_state = 6
** Random velocity drawn from the Maxwell-Boltzmann distribution (default)
i_initial_velo = 0
>>>>

<<<< annealing
tempk_init = 400.0 
tempk_last = 300.0
** number of temperature steps/time windows
n_time_change = 100
>>>>

**** Define molecular units (nearly same as chains) and states of simulated molecular system
<<<< unit_and_state
** Sequence information from PDB files
i_seq_read_style = 4
** Native-structure information used for Go model or its relatives from "native_info" files
i_go_native_read_style = 2
** Units and states of simulated system together with their molecular type
1    rna    input_cg.pdb
>>>>

**** Native (or reference) structure information for Go model and its relatives
<<<< native_info_sim1
NINFO(all/all) input.ninfo
>>>>

**** Specify the initial structures
<<<< initial_struct
** Specify the initial structures of all units
1 input_cg.pdb
>>>>

**** Set the energy function
<<<< energy_function
LOCAL(1)      L_GO
NLOCAL(1/1)   GO EXV ELE PAIR_RNA
i_triple_angle_term = 0
i_use_atom_protein = 0
i_use_atom_dna = 0
i_residue_exv_radii = 0
i_coef_from_ninfo = 1
>>>>

<<<< electrostatic
cutoff_ele = 20.0
ionic_strength = 0.15
diele_water = 78.0
i_diele = 0
>>>>

**** Define type of MD simualtion
<<<< md_information
** The number of steps of simulation
n_step_sim = 1
** The number of MD steps
n_tstep(1) = 100000000
** Time length in each MD step
tstep_size = 0.3
** Time steps for saving structural information
n_step_save = 10000
** Time steps for saving restart files
n_step_rst = 1000000
** Time steps for saving neighbor list
n_step_neighbor = 10000
** Temperature used in simulation
tempk = 300.0
** Seed of random numbers
n_seed = 81052434
** Do not fix the center of mass of the system at the origin
i_com_zeroing = 0
** Do not prohibit overall translation and rotation of the entire molecular system
i_no_trans_rot = 0
** Do not move the center of mass of initial strcutre to the origin (default)
i_com_zeroing_ini = 0
** Do not re-define some default parameters (default)
i_redef_para = 0
** Do not delete some interactions in a particular range (default)
i_del_int = 0
** Perform a simulation on a stage
i_stage = 1
** Perform flexible fitting to an AFM image
i_afm_fitting = 1
>>>>

**** Group for adding a stage potential
<<<< group
** All particles
GROUP(1) (1-629)
>>>>

**** Add a stage potential, which is Lennard-Jones type
<<<< stage
** Group of particles on which stage protential will affect
group_id = 1
** Stage position along the z axis
height = 0.0
** Cutoff distance relative to sigma parameter, which is the same values as EVX
cutoff_ratio = 2.5
** Epsilon parameter
eps = 1.2
** Uniform distance offset between particles and the stage
distance_offset = 2.0
>>>>

**** Perform flexible fitting to an AFM image
<<<< afm_fitting
** Strength of the potential; k=kappa*N*kB*T=1.00*629*0.001987*300
k       =  374.9469
** Softmax accuracy
beta    =  1.0
** Gaussian width along x axis
sigma_x =  2.0
** Gaussian width along y axis
sigma_y =  2.0
** Stage position
z0      =  0.0
** Cutoff for Gaussian
cutoff_sigma =  5.0

** Size of an AFM image [pixels]
n_x = 64
n_y = 63
** Size of a pixel [Angstrom]
pixel_size_x = 5.2
pixel_size_y = 5.2

** Group of particles on which AFM interaction affect
group_id = 1

** Informaion on AFM image: heights of all pixels
