[gmx-users] Modeling of the shear flow of the liquid using DEFORM

Own 12121325 own12121325 at gmail.com
Wed Sep 6 15:42:16 CEST 2017

Dear GROMACS users,

I would like to perform non-equilibrium simulation adding a shear flow on
the liquid in my bio-membrane system composed of lipids and water. By means
of the applications of the deformations I would like to shear a water in
X-Y dimensions along the surface of the membrane. Assuming that I make
modeling of the system in NPT ensemble with anisotropic coupling, will the
following options be correct for the setup?

compressibility = 0 0 4.5e-5 0.0 0.0 0.0 # here I sen compressibility for
all of the deformed directions xx, yy, xy etc to zero
ref_p           = 1.0135 1.0135 1.0135 0.0 0.0 0.0
; Deformation is on
Deform = 0 0 0 0.01 0.01 0.01 # here I add vel. 0.01 nm ps to the
non-diagonal elements corresponded to x and y dimensions of the box to
shear a liquid along it

Thanks so much for help!


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