Dear Gromacs users!
I have small question about order of the runs and input data. Ussually I do 2 equilibration phases and subsequent productive phase in the conditions wich are equal to the last equilibration phase ( e.g often this is npt ). In the second equil.mdp and md.mdp there is option continuation = yes which means that there have been previous phases of the simulation from wich coordinates and velocities should be taken. As I understood the coordinates is taken from .gro file but from what file the velocities must be providen ? Does it .cpt checkpoint file from previous run? In some cases I've forgotten to define -t npt.cpt for my MD run providing only coordinates in GRO file, topology and md.mdp but I have not seen any errors in such simulation due to absence of that .cpt and GROMPP never remind me of the absense of this file. What exactly is in that .cpt file and from wich source the velocities from equilibration phase are taken ? James
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