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 -- Gromacs Users mailing list
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