[gmx-users] PMF using umbrella sampling and Gromacs 5.0

Eudes Fileti fileti at gmail.com
Sun Jul 19 03:06:43 CEST 2015

Hello guys, I'm trying to calculate the PMF using umbrella sampling for a
small molecule to penetrate a lipid membrane. The 1D reaction coordinate is
along the z axis, which corresponds to the bilayer normal. The umbrella
potential acts on the center of mass of the molecule. The initial
configurations for each window, separated by a distance of 0.1nm, in a
range of 4 nm (distance between the centers of mass of the membrane and the
molecule), were obtained by a SMD.

The umbrella potential was applied according to the parameters below (for
Gromacs version 5.0.3). Each window was sampled by 5 ns.

pull                     = umbrella
pull_geometry            = direction
pull_dim                 = N N Y
pull_start               = yes
pull-print-reference     = no
pull_nstxout             = 1000
pull_nstfout             = 1000
pull_ngroups             = 2
pull-ncoords             = 1
; Group name, weight (default all 1), vector, init, rate (nm/ps),
pull-group1-name         = DPPC     ;  ref
pull-group2-name         = LIG         ;  pulled
pull-coord1-groups       = 1  2
pull-coord1-origin       = 0 0 0
pull-coord1-vec          = 0 0 1
pull-coord1-init         = 0
pull-coord1-rate         = 0.0
pull-coord1-k            = 3000

Histograms and the PMF obtained are shown in figure the link below.

I repeated the same test using other parameters (larger and small k values)
and options (cylinder and position, for this later I have used gmx 4.6) and
so far I could not get a satisfactory profile. In all tests, a problem that
I have observed is that the region near z = 0 is not sampled (there is a
gap between 0.0 and 0.5 nm). In addition the profile presents not smooth,
but somehow oscillating mainly for large z.

As the gmx distance give a value different of zero for the smallest
distance of separation between the centers of mass (around 0.1-0.2 nm) I
believe that this weird behavior is related to the reference distance that
I have used.

Could someone give me a light? Most of the tips I read in GMX list are
related to previous versions of the Gromacs and in a way the other tips
were already included in my tests.

Thank you

Eudes Eterno Fileti
Instituto de Ciência e Tecnologia da UNIFESP
Rua Talim, 330, São José dos Campos - SP
Página: sites.google.com/site/fileti/

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