Dear all, This may sound stupid, but just to make sure that I am right track about implicit solvent simulations, the set up involves pdb2gmx editconf grompp
I mean, we still need to define the box dimensions by editconf and apply periodicity, right? Besides, what type of ensemble would be a good choice (NPT, NVT, etc)? Best, -- Elif Nihal Korkmaz Research Assistant University of Wisconsin - Biophysics Member of Qiang Cui & Thomas Record Labs 1101 University Ave, Rm. 8359 Madison, WI 53706 Phone: 608-265-3644 Email: kork...@wisc.edu
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