> >>you can also use ptraj to extract the last frame of the trajectory
> >>to a restart format and just reinitialize the velocities using either the
> >>forces or a random number.
> >
> >In this case you would have to re-equilibrate since you
> >would be cold-starting at 0K.
>
> It depends on what you mean by "equilibrate". Certainly the structure
> itself has already adjusted to the simulation environment. By comparison,
> getting the velocities to re-equilibrate is much more rapid (~1ps),
> depending on the bath coupling constant.
This is good news. I don't know if there are any circumstances
where one would need a continuous trajectory, but if so the
complete reassignment/equilibration of velocities would qualify
as a new trajectory.
Bill
> Also, "cold start" only applies when using forces to get the initial
> velocities.
> If you use tempi>0, it's not a cold start and is identical to the Andersen
> thermostat.
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Received on Sun Sep 04 2005 - 00:53:01 PDT
