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Issues about the calculation of solvation free energy in organic solvent
Hi,
I am new to study YANK for the calculation of NaTFSI solvation free energy in 1,2-Dimethoxyethane (DME). So, I designed the system using .gro
file and .top
file.
Here is the .yaml file:
---
options:
minimize: yes
verbose: yes
output_dir: results
platform: CUDA
temperature: 298*kelvin
pressure: 1*atmosphere
checkpoint_interval: 50
systems:
dme-system:
phase1_path: [natfsi_dme_mix.gro, ./top/natfsi_dme_mix.top]
phase2_path: [natfsi.gro, ./top/natfsi.top]
ligand_dsl: resid 1
solvent_dsl: resname DME
solvent1: liquid
solvent2: gas
solvents:
liquid:
nonbonded_method: PME
nonbonded_cutoff: 10*angstroms
clearance: 16*angstroms
gas:
nonbonded_method: NoCutoff
protocols:
hydration-protocol:
solvent1:
alchemical_path:
lambda_electrostatics: [1.00, 0.75, 0.50, 0.25, 0.00, 0.00, 0.00, 0.00, 0.00, 0.00, 0.00, 0.00, 0.00, 0.00, 0.00, 0.00, 0.00, 0.00, 0.00]
lambda_sterics: [1.00, 1.00, 1.00, 1.00, 1.00, 0.95, 0.90, 0.85, 0.80, 0.75, 0.70, 0.65, 0.60, 0.50, 0.40, 0.30, 0.20, 0.10, 0.00]
solvent2:
alchemical_path:
lambda_electrostatics: [1.00, 0.75, 0.50, 0.25, 0.00, 0.00, 0.00, 0.00, 0.00, 0.00, 0.00, 0.00, 0.00, 0.00, 0.00, 0.00, 0.00, 0.00, 0.00]
lambda_sterics: [1.00, 1.00, 1.00, 1.00, 1.00, 0.95, 0.90, 0.85, 0.80, 0.75, 0.70, 0.65, 0.60, 0.50, 0.40, 0.30, 0.20, 0.10, 0.00]
experiments:
system: dme-system
protocol: hydration-protocol
natfsi.gro
contains one NaTFSI molecule. natfsi_dme_mix.gro
contain one NaTFSI molecule and 6000 DME molecule.
Then I got the results. But it seems wierd for the reason that most solvation free energy is < 0 .
Free energy of solvation: 69.346 +- 0.594 kT (41.066 +- 0.352 kcal/mol)
DeltaG solvent1 : -9.227 +- 0.460 kT
DeltaG standard state correction: 6.437 kT
DeltaG solvent2 : 66.556 +- 0.376 kT
Enthalpy of solvation : 139.169 +- 98.876 kT (82.414 +- 58.553 kcal/mol)
Is the system I designed to calculate the free energy of solvation reasonable? Or should I set a single molecule of NaTFSI as phase1_path
and mixture as phase2_path
? Any suggestion or tips would be apperciated.
Best, Drep.