##################################################################################
#
# EMIL module for calculation of absolute free energies of biomolecules.
# By Joshua T Berryman, University of Luxembourg, 2013.
#
# This code is covered by the GPL, except when distributed with non-gpl parts of
# AMBER (when it is covered by the same licence as the rest of that distribution).
# See licence.txt in the source directory.
#
# If you use this module for research, please cite:
#                         Joshua T Berryman and Tanja Schilling,
#                         J. Chem. Theory Comput., 2013, 9 (1), 679-686.
#
#
##################################################################################
# Setting up emil, with fake boxinfo: 45.0079 30.9682 34.0451
# read parameters:
# N 444
# seed 1902 Displ 0.2
#
# Setting well types
# marking 220 of 444 atoms as heavy
# matching 1 atoms as chain roots
# mask ACE,CYS,SER,ALA,LEU,ILE,THR,VAL,ASN,ASH,NME sets type of 444 atom wells as 1 of 7
#
# Initialising wells
# Well type Einstein Molecule has parameters:
#   r s.t. E=0: 1
#   epsilon:    5
#   A/well:    -4.30294
#
#
# Reading well positions from wellsIn.dat
# msd part-well is: 0
# Finished setting particle well types:
# Null              0
# Einstein Molecule 444
# Conewell Liquid   0
# Harmonic Liquid   0
# Wingwell Liquid   0
# Wobblium          0
# Relative position 0
# 444 heavy or solute atoms.
# Building well neighbour list. 
# Linking particles to wells. 
# Linked particles to wells, rms distance (heavies): 0
# N heavies or roots: 444
# done setup.
#
# Energy units: initial beta  1.67741 == 1.0 / 0.596158
# Scaling forces using polynomial mixing functions, at lambda = 0.9 :
# scaling amber forces by 0
# scaling soft force by   3.69056e-05
# scaling EMIL forces by  0.81
# Uncorrected EABS is: -2220
# With offset of 0 this is: -2220
#
# Reporting EMIL abstract Helmholtz free energy,
# according to equations in supp. data of Berryman & Schilling, JCTC 2013: 
# Total free energy A of abstract model (units kT): -1.910504e+03
# A-Solid: -1.910504e+03 A-Liquid: 0.000000e+00 A-degen: 0.000000e+00
#
# Total free energy A of abstract model (units of calling program): -1.138962e+03
# A-Solid: -1.138962e+03 A-Liquid: 0.000000e+00 A-degen: 0.000000e+00
#
#
# Generalised forces will be reported in units of calling program, not in kT/A
#
# emil mol_lambda: 0.9 abstract_lambda: 0.9
#
# (mixed)  ABS_ENTH(kT) -1798.2 MOL_ENTH 0 TOT      -1798.2
# (native) ABS_ENTH(kT) -2220 MOL_ENTH 0 TOT      -2220
#
nstep:  0 soft_dHdL:  -3.63219795e+02 molec_dHdL:  0.00000000e+00 abstr_dHdL:  -2.38224539e+03
nstep:  10 soft_dHdL:  -3.62638271e+02 molec_dHdL:  0.00000000e+00 abstr_dHdL:  -2.36472746e+03
nstep:  20 soft_dHdL:  -3.60160205e+02 molec_dHdL:  0.00000000e+00 abstr_dHdL:  -2.28296548e+03
nstep:  30 soft_dHdL:  -3.57715856e+02 molec_dHdL:  0.00000000e+00 abstr_dHdL:  -2.17771261e+03
nstep:  40 soft_dHdL:  -3.56820754e+02 molec_dHdL:  0.00000000e+00 abstr_dHdL:  -2.11402753e+03
nstep:  50 soft_dHdL:  -3.57691092e+02 molec_dHdL:  0.00000000e+00 abstr_dHdL:  -2.12125862e+03
nstep:  60 soft_dHdL:  -3.60073029e+02 molec_dHdL:  0.00000000e+00 abstr_dHdL:  -2.17017603e+03
nstep:  70 soft_dHdL:  -3.62916828e+02 molec_dHdL:  0.00000000e+00 abstr_dHdL:  -2.19941172e+03
nstep:  80 soft_dHdL:  -3.64382359e+02 molec_dHdL:  0.00000000e+00 abstr_dHdL:  -2.16439739e+03
nstep:  90 soft_dHdL:  -3.64569601e+02 molec_dHdL:  0.00000000e+00 abstr_dHdL:  -2.06692483e+03