[gmx-users] Slowly changing the q and vdw interactions for free energy calculations
qasimpars at gmail.com
Fri May 4 16:42:59 CEST 2018
Any comments on my questions?
> On 3 May 2018, at 19:48, Qasim Pars <qasimpars at gmail.com> wrote:
> Dear users,
> 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.
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