CB8.txt

# Results for CB8
#
# This file will be automatically parsed.  It must contain the following four elements: predictions, name of method, software listing, and method.
# These elements must be provided in the order shown. 
#
# The data in each prediction line should be structured as follows, with all (up to six) numbers in kcal/mol.
# Guest ID, Free energy, free energy SEM, free energy method error, enthalpy, enthalpy SEM, enthalpy method uncertainty
# The list of predictions must begin with the "Prediction:" keyword, as illustrated here.
Predictions:
CB8-G0, -10.1,,,  -0.3,, 
CB8-G1, -10.5,,,  -20.5,, 
CB8-G2, -5.4,,,   -2.9,,
CB8-G3, -2.3,,,   -5.0,,
CB8-G4, -8.9,,,   -12.1,,
CB8-G5, -1.4,,,   -1.8,,
CB8-G6, -9.2,,,   -0.8,,
CB8-G7, -2.3,,,   -5.0,,
CB8-G8, -8.9,,,   -12.1,,
CB8-G9, -1.4,,,   -1.8,,
CB8-G10, -9.2,,,   -0.8,,
CB8-G11, -6.2,,,   -0.4,,
CB8-G12, -8.2,,,   -0.3,,
CB8-G13, -7.2,,,   -0.6,,
#
# Please provide an informal yet informative name of the method used.
# The "Name:" keyword is required, as shown here.
Name:
Long/DDM/GAFF/TIP3P
#
# All major software packages used and their versions
# The "Software:" keyword is required.
Software: 
Gromacs 5.0.2
Gaussian 09
#
# Methodology and computational details. 
# Level of detail should be at least that used in a publication.  
# Please include the values of key parameters, with units, and explain how any statistical uncertainties were estimated.
# 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: 
All simulations were performed with the pmemd.cuda program from
AMBER14, using our attach-pull-release method (10.1002/jcc.23398,
10.1021/acs.jctc.5b00405). Ten windows were used for the attach phase,
and umbrella sampling windows during the pull phase were spaced at 1
Angstrom intervals, and extended to a maximum distance of 25
Angstroms. As no restraints were added to the host itself, the work of
release could be computed purely analytically.

Each sampling window included a minimum of 50 ns simulation time, with
extension as needed to bring the standard error estimate of the
overall free energy within 0.5 kcal/mol. The longest sampling required
in any window was 125 ns. The bonded and initial Lennard-Jones
parameters were obtained from GAFF. Partial atomic charges were
generated with the RESP procedures as implemented in the program
Antechamber. Sodium or chloride counterions, with parameters from
Joung and Cheatham (10.1021/jp8001614), were added only as needed to
neutralize the total charge of each host-guest system; no additional
counterions were added. The starting structures were obtained by
docking from MOE initially, but were relaxed through short preliminary
MD simulations. Each system was solvated with ~2000 TIP3P waters in an
orthorhombic box whose dimensions were approximately 36 x 36 x 52
cubic Angstroms.

Production simulations were run in the NPT ensemble, with temperature
control using a Langevin thermostat with collision frequency 1.0 ps-1
and pressure control provided by the Monte Carlo barostat. Direct
space nonbonded interactions were truncated with a 9.0 Angstrom cutoff,
whereas long-range electrostatics were handled with the PME method,
using default AMBER settings. SHAKE constraints were applied to bonds
involving hydrogen, and the simulation time step was set to 2 fs.