AMBER Archive (2005)

Subject: Re: AMBER: STARTING WHERE I LEFT OFF

From: Carlos Simmerling (carlos_at_ilion.bio.sunysb.edu)
Date: Sat Sep 03 2005 - 13:28:27 CDT

Bill Ross wrote:

>>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.

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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