[gmx-users] pmf settings

Qasim Pars qasimpars at gmail.com
Thu Nov 17 11:38:40 CET 2016

Dear users,

I am trying to calculate the binding free energy between protein and ligand
using the PMF. I will add the below pull code lines to my production run
mdp file.

pull            = umbrella
pull_geometry   = distance
pull_dim        = Y Y Y
pull_start      = yes
pull_ngroups    = 2
pull_group0     = protein
pull_group1     = ligand
pull_init1      = 0
pull_rate1      = 0.0
pull_k1         = 5000
pull_nstxout    = 1000
pull_nstfout    = 1000

My questions are:

-According to the above lines the binding free energy is calculated for the
center of mass of each group, right?

-Is it necessary to add the above lines in the nvt.mdp and npt.mdp file as

-how can I set/change the number of windows used in the Umbrella Sampling

-To get the accurate binding energy should I use some specific atoms of
each group (for instance: ligand N1 and protein C15) or the center of mass
of each group?

Hope someone will answer the questions.

Qasim Pars

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