On Thu, Oct 14, 2010, Daniel Roe wrote:
>
> Restart files can contain only coordinates, or they can contain
> coordinates and velocities (see
> http://ambermd.org/formats.html#restart for complete details). When
> you run a minimization you are not generating any velocities which is
> why the last part of your restart file contains the zeros.
Maybe, maybe not. Restarts from minimizations don't have velocities, which is
different from having zeros for velocities. Basically, we need more details
about what is meant by your statement that "the last coordinates in the
restart file are 0.00". How many last coordinates? Did you count the total
number of entires in the restart file? What about the box size information,
which is always at the end of the restart file for a periodic system?
I am concerned that you have solvent (water?) in your system, yet are not
using SHAKE. This can cause bad energies, but would show up as bad energies
in your mdout file. Basically, we're just guessing here about what is really
happening.
....dac
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Received on Thu Oct 14 2010 - 06:00:02 PDT
