Dear David,
yes it really helped. Thank you so much for your detailed answer.
David A Case <david.case.rutgers.edu>, 13 Nis 2020 Pzt, 22:22 tarihinde
şunu yazdı:
> On Mon, Apr 13, 2020, Erdem Yeler wrote:
>
> >1) What is the integration algorithm is it velocity, Verlet or
> leap-frog?
>
> Actually, both and neither. For a simple system, the two methods will
> give equivalent trajectories in the limit of infinite precison
> arithmetic. Once you add SHAKE (bond length constraints) and any sort
> of thermostat or barostat, then the distinctions between the two methods
> become quite technical and harder to just label as one or the other.
>
> Sander's implementation is closer to velocity Verlet, since we
> propagate velocities in two (half-time) steps, rather than as a single
> (full-time) step, as in the original Leapfrog method. But the external
> interface still uses velocities on the half-step, for backwards
> compatibility with the original leapfrog implementation, which dates
> back to about 1979.
>
> ...hope this helps...dac
>
>
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Received on Tue Apr 14 2020 - 13:00:02 PDT
