So would it be reasonable to set rcoulomb = 2 or even 3 nm when rerunning a trajectory? I am looking at a ligand-antibody system, and I guess the long-range electrostatic interactions will not be small.
A trick proposed by Nicolas in the mailing list during 2007 is to set charges to 0.00 for everything except the atoms we are interested in. This would make Coul-LR: = Coul.-recip., which is calculated by PME (more accurate than just setting rcoulomb to 3nm?) and we can read from .edr file. So I wonder if this method is theoretically sound? Thanks, Yun
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