Dear Amber users
I am running a homodimer protein for 100 ns. Upon 65 ns simulation, the
dimer has dissociated to two monomers (no problem). The 1st monomer has
nearly moved out the water simulation box. In the next 15 ns this monomer
alternates between outside and inside the simulation box to form the dimer
again. Does this movement outside the box affect the subsequent
calculations? And if so can I re-image the dimer and re-run the simulation
process at the time of separation?. I am using the ff14SB forcefield and
the medium of simulation is physiological saline. The Amber version is
AMBER16.
Please, any help is thankful
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Received on Thu Jan 09 2025 - 10:00:02 PST
