Dear gromacs users, I performed a Hemiltonian Replica Exchange (i.e. replica exchange where each replica has a init_lambda=0, delta_lambda=0 and init_lambda ranging uniformely from 0 to 1).
Since I have only ten fixed discrete lambda, I run a Temperature Replica Exchange where, for each replica I generated a .top file with the parameter rescaled through a python script ( in practice I did through python the same thing gromacs is supposed to do with the H-REM previously described). Now gromacs complained because every replica has the same setup, so I changed the temperatures using very close values (300.0001K, 300.0002K,300.0003K,300.0004K,300.0005K,300.0006K,300.0007K,300.0008K, 300.0009K) With this setup the simulation runs fine and I expect to have similar result. Then I compared the results observing two phenomena: 1) In the second case exchange rate is 100%, while in the first case I have an exchange rate close to 30%. Does it rise because the temperatures are too close? 2) The second setup is 3x faster! In particular I observe an imbalance between PME and force calculation ranging from 10% to 60%. I tried to run each replia indipendently (a different mdrun instance for each .tpr file) but still I observe the same performance slowdown. I guess the free energy impairs the efficient force calculation, but I dont understand why. Can someone explain me the two observations? Francesco
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