[gmx-users] NEMD of membrane protein

[RAGHUVAMSI P V]

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
questions:
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
simulation.
Thanks in advance
Raghuvamsi
IIT Hyderabad
Dept. Of Biotechnology