If I have continuation = no in mdrun, does it mean I broke the ensemble and therefore the time-dependent properties are unreliable?
Even if the -cpi option is mentioned (with the previous cpt file), would it not take velocities from the cpt file?
At what point does it reassign the velocities - only at the start - when mdrun is performed, or every time the mdrun is performed (for instance running after wall-time on the server is over)
Please help.
The continuation keyword tells mdrun whether or not constraints need to be solved in the first step of the run. When set to “no,” mdrun will constrain the initial coordinates because it assumes no constraints had been previously applied. If your previous simulation was performed in the presence of constraints, presumably nothing will really change, however it is possible that minor alterations would be made to the coordinates, though I doubt the magnitude would be anything that would affect the simulation.
Thank you so much for this clarification Dr. Lemkul.
Does this apply also to the gen_vel option?
I guess not, gen_vel = yes in mdrun, will break the ensemble?
Yes, that will randomize velocities and break continuity.
OK. Thank you.