Hi Hess,
Thank you for your answer. I am planning to perform TI on an elongated molecule called C12EO8 with a maximum molecular length of about 2.3 nm.
Is this molecule a “large molecule”?
I am also planning to calculate TI under the following conditions.
I understand that if I calculate with couple-intramol=yes, the Van der Waals and Coulomb interactions within the molecule will also be turned on and off, is this correct?
free-energy = yes
couple-moltype = LIG
couple-lambda0 = vdw-q
couple-lambda1 = none
couple-intramol = no
separate-dhdl-file = yes
sc-alpha = 0.5
sc-power = 1
sc-sigma = 0.3
init-lambda-state = “each lambda point”
coul-lambdas = 0.0 0.1 0.2 0.3 0.4 0.5 0.6 0.7 0.8 0.9 1.0 1.0 1.0 1.0 1.0 1.0 1.0 1.00 1.0 1.00 1.0 1.00 1.0 1.00 1.0
vdw-lambdas = 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.1 0.2 0.3 0.4 0.5 0.6 0.65 0.7 0.75 0.8 0.85 0.9 0.95 1.0
nstdhdl = 100
calc-lambda-neighbors = -1