Restoring simulation from the previous run

From: James Starlight (
Date: Wed Mar 19 2014 - 03:32:31 CDT

Dear NAMD users!

I wounder to know does it possible to perform simulation beginning from the
coordinates and velocities of the already finished simulation with the
introduction of the changing to the atomic contain of the system (adding
ligands or ions)?

For instance I've simulated 100ns of the apo form of my protein and then
add ligand to the conformation of this protein which I've obtained at the
end of the apo simulation. Can I run new (holo system) simulation with the
velocities set from the previous run defining new velocities distribution
only for ligand ?

Thanks for help,


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