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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:
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.
The text was updated successfully, but these errors were encountered:
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:
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 .
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 asphase2_path
? Any suggestion or tips would be apperciated.Best,
Drep.
The text was updated successfully, but these errors were encountered: