[gmx-users] MD after equilibration phase

James Starlight jmsstarlight at gmail.com
Fri Apr 6 09:05:51 CEST 2012

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 ?

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