#
#  Example of calculation of solvation free energy of a lidocaine 
#  molecule in water (in 500 SPC-f water molecules in a periodic box)
#
#  This input file should be renamed in md.input in case of  parallel execution
#
Main_filename lidocaine_h2o
Verbose_level 5
Read_restart no
Dump_restart 1000000
Check_only no
#  Here we define 2 molecular types:
#  lidocaine (one molecule) and water (500 molecules)
Molecule_types 2
lidocaine      1
H2O	      500
#  Here .mmol files for water and lidocaine must be present
Path_DB .
Change_V no
Change_T no
#  Define temperature and termostat relaxation time
Nose_thermostat 298. 30.
#  Define pressure and barostat relaxation time (fs)
Barostate_NH 1. 1000.
PBC rect
#  Periodically remove center of mass motion 
COM_check yes 50000
#
# We would like to run with 2fs (long) time step for 20ns total
Time_step 2.
Number_steps 10000000
#  short time step will be 0.2 fs
Double_timestep 10
#  total cutoff
R_cutoff 12.
R_short 5.
Neighbour_list 10
Electrostatics Ewald 2.8 8.
# Cut eventual large forces at start (for removing overlappings)
Cut_forces 0.5
# produce a line at output each 5000 steps
Output 5000
# take averages (including subensemble distribution) each 20 steps
Average_freq 20
#  make series of 500000 steps (1ns)
Serie_avegare 500000
Average_from 11
#
Startup FCC
Dump_XMOL yes
#  EE:  we define 35 subensembles; automatic optimization
MDEE  35  auto
#  We apply expande ensemble to the first molecule type (lidocaine)
EE_typ 1
#  Number of Wang-Landau iterations may be eventually increased from default 10
# Num_WL 12
End
