[gmx-users] Slowly changing the q and vdw interactions for free energy calculations
qasimpars at gmail.com
Thu May 3 18:48:21 CEST 2018
For the binding free energy calculations I would slowly first turn off the coulomb interactions, and then the vdw interactions at only one production step of 1 ns (not multiple simulations as in MBAR). My questions are:
Can I do that with gromacs?
I don't know whether the following settings are correct or not?
According to the following settings the simulation time between two lambda states will be 100 ps, right? Or do I need to use delta-lamda?
free-energy = yes
init-lambda = 0
coul-lambdas = 0.0 0.1 0.2 0.5 1.0 1.0 1.0 1.0 1.0 1.0
vdw-lambdas = 0.0 0.0 0.0 0.0 0.0 0.2 0.4 0.6 0.8 1.0
sc-alpha = 0.5
sc-power = 1
sc-sigma = 0.3
couple-moltype = ligand
couple-lambda0 = vdw-q
couple-lambda1 = none
couple-intramol = no
nstdhdl = 1
Any help will be appreciated.
More information about the gromacs.org_gmx-users