##################################################################################
#
# 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
#
# 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:  -609.268 molec_dHdL:  0.000 abstr_dHdL:  -3996.000
nstep:  10 soft_dHdL:  -608.293 molec_dHdL:  0.000 abstr_dHdL:  -3966.615
nstep:  20 soft_dHdL:  -604.136 molec_dHdL:  0.000 abstr_dHdL:  -3829.467
nstep:  30 soft_dHdL:  -600.036 molec_dHdL:  0.000 abstr_dHdL:  -3652.915
nstep:  40 soft_dHdL:  -598.534 molec_dHdL:  0.000 abstr_dHdL:  -3546.089
nstep:  50 soft_dHdL:  -599.994 molec_dHdL:  0.000 abstr_dHdL:  -3558.218
nstep:  60 soft_dHdL:  -603.990 molec_dHdL:  0.000 abstr_dHdL:  -3640.273
nstep:  70 soft_dHdL:  -608.760 molec_dHdL:  0.000 abstr_dHdL:  -3689.313
nstep:  80 soft_dHdL:  -611.218 molec_dHdL:  0.000 abstr_dHdL:  -3630.580
nstep:  90 soft_dHdL:  -611.532 molec_dHdL:  0.000 abstr_dHdL:  -3467.078