Hey Justin, thanks for your reply. For gen_vel, the manual says "Generate velocities in grompp according to a Maxwell distribution at temperature gen_temp [K], with random seed gen_seed. This is only meaningful with integrator md" Since the integrator I am using is sd, I put 'gen_vel no' Yes you are correct, this is equilibration. >From what you are saying, even with sd as the integrator, I guess, I should put gen_vel yes gen_temp 310 ; i want to do the simulation at 310K
thanks -- Shyno Mathew PhD student Department of Chemical Engineering Columbia University
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