# WATER-TOLUENE (ΔG_toluene - ΔG_water) TRANSFER FREE ENERGY PREDICTIONS
#
# This file will be automatically parsed. It must contain the following four elements:
# predictions, name of method, software listing, and method description.
# These elements must be provided in the order shown with their respective headers.
#
# Any line that begins with a # is considered a comment and will be ignored when parsing.
#
# 
# PREDICTION SECTION
#
# the following is transfer free energy form water to toluene, i.e.
# DG(toluene) - DG(water), where DG is the solvation  energy, i.e. the free energy of
# transferring a molecule from gas-phase to the solvent. 
Predictions:
SAMPL9-1,-4.0,0.7,2.
SAMPL9-2,-5.1,0.8,2.
SAMPL9-3,-7.7,0.5,2.
SAMPL9-4,-8.2,0.6,2.
SAMPL9-5,-5.5,0.7,2.
SAMPL9-6,2.8,0.5,2.
SAMPL9-7,-7.7,1.1,2.
SAMPL9-8,1.3,2.1,2.
SAMPL9-9,-7.8,0.7,2.
SAMPL9-10,-5.0,0.4,2.
SAMPL9-11,-1.9,0.9,2.
SAMPL9-12,1.3,0.9,2.
SAMPL9-13,-2.9,0.7,2.
SAMPL9-14,-5.3,0.5,2.
SAMPL9-15,1.5,1.3,2.
SAMPL9-16,-2.6,1.4,2.
#
#
#
# Please list your name, using only UTF-8 characters as described above. The "Participant name:" entry is required.
Participant name:
Piero Procacci

#
#
# Please list your organization/affiliation, using only UTF-8 characters as described above.
Participant organization:
University of Florence (Italy)

#
#
# NAME SECTION
#
# Please provide an informal but informative name of the method used.
# The name must not exceed 40 characters.
# The 'Name:' keyword is required as shown here.
Name:
(NE-FG) NonEquilibrium Fast Growth 
#
#
# COMPUTE TIME SECTION
#
# Please provide the average compute time across all of the molecules.
# For physical methods, report the GPU and/or CPU compute time in hours.
# For empirical methods, report the query time in hours.
# Create a new line for each processor type.
# The 'Compute time:' keyword is required as shown here.
Compute time:
1.5 hours (wall time) per molecule solvation free energy using 12 cluster nodes (CPU-only) 

#
# COMPUTING AND HARDWARE SECTION
#
# Please provide details of the computing resources that were used to train models and make predictions.
# Please specify compute time for training models and querying separately for empirical prediction methods.
# Provide a detailed description of the hardware used to run the simulations.
# The 'Computing and hardware:' keyword is required as shown here.
Computing and hardware:
CRESCO6 cluster (Intel(R) Xeon(R) Platinum 8160 2.10GHz24x2 cores)
https://www.eneagrid.enea.it/Resources/CRESCO_documents/CRESCO/Sezione6.html

# SOFTWARE SECTION
#
# List all major software packages used and their versions.
# Create a new line for each software.
# The 'Software:' keyword is required.
Software:
ORAC6.1 http://www1.chim.unifi.it/orac/

# METHOD CATEGORY SECTION
#
# State which method category your prediction method is better described as:
# `Physical (MM)`, `Physical (QM)`, `Empirical`, or `Mixed`.
# Pick only one category label.
# The `Category:` keyword is required.
Category:
physical (MM)

# METHOD DESCRIPTION SECTION
#
# Methodology and computational details.
# Level of details should be roughly equivalent to that used in a publication.
# Please include the values of key parameters with units.
# Please explain how statistical uncertainties were estimated.
#
# If you have evaluated additional microstates, please report their SMILES strings and populations of all the microstates in this section.
# If you used a microstate other than the challenge provided microstate (`SMXX_micro000`), please list your chosen `Molecule ID` (in the form of `SMXX_extra001`) along with the SMILES string in your methods description.
#
# Use as many lines of text as you need.
# All text following the 'Method:' keyword will be regarded as part of your free text methods description.

Method:
Force field for solute is GAFF2 with AM1-BCC charges (generated with
PrimaDORAC www1.chim.unifi.it/orac/primadorac); Starting
nonequilibrium state is prepared by combining 96 configurations of the
gas-phase solute sampled with Hamiltonian Replica Exchange (minimum
scaling factor 0.1 -> T=3000 K) combined with 96 configuration of pure
solvent in standard conditions (NPT). Gas-phase HREM simulations were
run for 8 ns. MD simulations of pure solvent were run for 5 ns.
Solute molecules are in their neutral state. For the solvent, we used
343 Toluene molecules in a cubic box (GAFF2-AM1-BCC) with a mean
side-length of 39.72 Angs and 1728 OPC3 water molecules in a cubic box
with a mean side-length of 37.45 Angs. In the 100 NE alchemy runs, the
initially decoupled solute was recoupled in the solvent (NPT
condition) in 450 ps. The solvation free energies DG_w and DG_t are
evaluated using the Gaussian estimate if the p-value of the
Anderson-Darling test of the work distribution is greater than 50% or
with the Jarzynski estimate DG=-RT ln(e^{-\beta W} with bias estimated
from the variance. Errors (confidence interval 95%) are computed with
bootstrap with resampling. The Toluene-water partition coefficient is
computed as LogTW= -(DG_t -DG_w )/RT/log(10).  The water to toluene
transfer free energy is DG_t - DG_w.  Calculation were done on the
ENEA-CRESCO6 cluster in Portici (NA), Italy using the program ORAC
(www1.chim.unifi.it/orac ). Wall-clock time for a full LogTW
calculation, on a per solute basis, was ~ 1.5 hour using 12 48-cores
nodes (Skylake Intel(R) Xeon(R) Platinum 8160 2.10GHz).
#
#
# All submissions must either be ranked or non-ranked.
# Only one ranked submission per participant is allowed.
# Multiple ranked submissions from the same participant will not be judged.
# Non-ranked submissions are accepted so we can verify that they were made before the deadline.
# The "Ranked:" keyword is required, and expects a Boolean value (True/False)
Ranked:
True