[gmx-users] NEMD of membrane protein

RAGHUVAMSI P V bo15mtech11002 at iith.ac.in
Wed Aug 17 12:13:16 CEST 2016

Dear Sir,
           I'm trying to mimic osmotic pressure condition on a membrane
protein in gromacs by  applying constant force (through constant
accelearation) on group of water molecules in z-direction in the simulation
box through Non-equilibrium MD option in mdp file. I have following
i) Why cos-acceleration  and deform needed what is its role and in my
specific condition where I'm not inducing shear flow are those two
parameters need to be specified?
ii) Is it necessary to include energy group exclusion option by mentioning
freeze groups i.e protein and lipids (in my case) which i will be freezing
only in z-direction? Is it necessary for proper calculation of energy and
Thanks in advance
IIT Hyderabad
Dept. Of Biotechnology

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