I'd like to select individual frames from my equilibration run to start separate production runs. I've saved coordinates at various points of the equilibration and when using them to start the production runs I get an 'Energy Change Tolerance Exceeded ' error. I'm using an NPT ensemble and I'm thinking that the box size has changed which is resulting in the error. I was wondering if I could just read the equilibration restart file at a particular location in order to vary the starting point of the production run?
The restart file has complete information only for single time point, usually the last one in the corresponding trajectory file.
If you set up PBC via crystal first, you can read a single coordinate set directly from a trajectory file, and the unit cell size will be automatically updated. You would still have to assign new initial velocities in the usual way, however.
Another option is to save a velocity trajectory at the same frequency as coordinates, then read coordinates from the trajectory, read corresponding set of velocities into the COMP coordinate set, and use the DYNAmics option "IASVEL 0" to use those velocities to start a new simulation.