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I am generating a new tpr with grompp and a new mdp for second continuation of my simulation . In this mdp I am turning off gen velocity and since my 1st part of simulation ended at 20000ps and 10000000 steps : I am doing init-step as 10000000 and tinit as 20000 and doing continuation = on . My dt is 0.002 or 2fs .
The problem is my second simulation is staring at 10001000 steps but the time is 40000 ps somehow . I checked everything with gmx check , I tried extracting the last frame from the previous checkpoint file and then covert it into a gro file and with it generated a new tpr : but the simulation still will start at 40 ns . Please help .
So to be clear, what you’re trying to do is extract a frame from the middle of a previously run simulation and use that as the start of a new simulation, and the start of the simulation is specifying a the expected step but not the corresponding time, is that correct? Could you send the mdp files and commands you’re using to help with seeing what the problem might be?
Only suggestion I can think of right now is maybe try running without specifying tinit, since you already have the init-step specified and maybe specifying both is somehow causing problem