[gmx-developers] milestoning

[Sergio Decherchi]

Dear Gromacs Developers,
I would like to allow Gromacs to do Markovian Milestoning because it seems a very
effective algorithm for the estimation of both free energy and kinetics. To achieve
this goal I have to confine the simulation inside a Voronoi cell.
To do this confinment, in litterature it is suggested (see Venturoli and Vanden Eijden "Markovian Milestoning") that one can, upon Voronoi cell violation, invert velocities and reset the position to the previous integration step such that the system can remain inside the Voronoi cell.

I decided to interface to Gromacs via plumed2 such that collective variables can be
used to compute the metric that rules the Voronoi cell.

Following plumed2 philosophy I got velocities just before the do_force call in md.c.
Assuming a velocity verlet integrator which are the velocities that I get in this point of the code?
I mean, which time step?

Do you suggest a specific strategy to invert velocities and set the previous positions?

Gromacs expects an atom in a domain decomposition cell; after the reset of the position to the previous step, this cell may have changed thus leading to an inconsitency. I got this kind of problems.

How can I set the positions to the previous integration step and at the same time assuring
that Gromacs is aware of this change of positions from the domain decomposition stand point?

This problem can be avoided by using particle decomposition, but it is probably suboptimal.

I have done many trials and I have other issues.
Often lincs algorithm fails; when I compute
the 'reflection' on the Voronoi facet I use subset of atoms because the metric is defined in a
subset of atoms. To get the maximal stability should I change velocities and reset positions
of the whole system? Still lincs should be enabled or disabled at all?

Thanks,
Cheers,
Sergio Decherchi
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