AMBER Archive (2004)

Subject: Re: AMBER: restrt

From: Bill Ross (ross_at_cgl.ucsf.edu)
Date: Thu Jan 22 2004 - 11:15:58 CST

> The trajectory in mdcrd only contains coordinates. If you need the
> velocities, you need to save them by setting ntvel(?)=(e.g.)500. This will
> trigger saving of velocities to mdvel everything 500 steps. You then need
> to combine the velocities and coordinates to restrt.
>
> HOWEVER, if you start the simulations from the restrt files combined this
> way you will produce really the same trajectory delayed by (e.g.) 500
> steps (they will eventually diverge if the simulations are done on
> parallel machines).

The trajectories will also diverge on a single cpu because
the precision is highly truncated in the mdcrd/mdvel format.
This will happen even with the restrt format - only saving
the info in binary (machine-specific) form would overcome
this.

Bill Ross

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