[gmx-users] Time reversibility and settle
Berk Hess
gmx3 at hotmail.com
Fri May 13 08:50:58 CEST 2005
>Hello and thank you for your reply.
>However, my question about the time reversibility of a leap-frog integrator
>with settle (e.g. for TIP3P water molecules) was concerned with the
>actual implementation in Gromacs, rather than the analytical point
>of view. In other words, is this implementation of leap-frog +
>settle still time-reversible in the limit of infinite numerical
>accuracy?
>This question arises since I tried different numerical
>accuracies (single, double and quadruple precision numbers and
>operations; for the latter I had to rewrite large parts of the
>code...) with, in all cases, similar (and pretty large)
>deviations from the "forward" trajectory when reversing the time.
>On the other hand, just bypassing the "settle" subroutine
>(e.g. by commenting all the code related to the original
>implementation of settle by Miyamoto and Kollman), it works as
>expected: the algorithm is almost perfectly time-reversible
>and the only "noise" is due to numerical inaccuracies, with
>deviations comparable, in the three different cases (single,
>double, long double) to the accuracy of numbers.
>Thus, I'm trying to understand whether just resetting the position
>of atoms, as done in the current implementation of "settle",
>still leads to a time-reversible MD (in the limit of infinite
>machine accuracy).
>Any suggestion about that?
In the limit is should be time-reversible, unless there is a bug in
the settle algorithm, which I consider very unlikely.
Have you tried to use shake or lincs (with high precision settings)?
There could be some other issues, but when the unconstrained
dynamics is reversible you have probably taken care of these:
You should not use temperature and pressure coupling (the new
version will have reversible Nose-Hoover coupling).
When reversing you should take care to use the proper velocities,
as x(t), v(t-t/2dt) is stored you need to take the velocities from
the next step when reversing.
Berk.
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