Yes, my plan was to add that after the langevin only move works.
On Jan 9, 2014 9:12 PM, "John Chodera" <notifications@github.com> wrote:

> In repex/replica_exchange.py:
>
> > -        # Run dynamics.
> > -        integrator.step(self.nsteps_per_iteration)
> > -        integrator_end_time = time.time()
> > -        # Store final coordinates
> > -        getstate_start_time = time.time()
> > -        openmm_state = context.getState(getPositions=True)
> > -        getstate_end_time = time.time()
> > -        self.replica_coordinates[replica_index] = openmm_state.getPositions(asNumpy=True)
> > -        # Store box vectors.
> > -        self.replica_box_vectors[replica_index] = openmm_state.getPeriodicBoxVectors(asNumpy=True)
> > -
> > +        thermodynamic_state = self.thermodynamic_states[state_index] # thermodynamic state
> > +        sampler_state = self.sampler_states[state_index]
> > +
> > +        move = mcmc.LangevinDynamicsMove(nsteps=self.nsteps_per_iteration, timestep=self.timestep, collision_rate=self.collision_rate)
> > +        new_sampler_state = move.apply(thermodynamic_state, sampler_state)
>
> Looks like you're just using LanegvinDynamicsMove to replace the old
> Langevin dynamics integrator internally.
>
> I think we want to have ReplicaExchange specify a default MCMC move_set,
> where the user can replace it with their own via accessing repex_simulation.move_set
> = ... if they wish.
>
> The MCMC scheme is intended to be used by creating an MCMCSampler with
> this move_set, and then calling apply(), like this:
>
> # Create MCMC samplersampler = MCMCSampler(thermodynamic_state, move_set=move_set)# Run a number of iterations of the sampler.updated_sampler_state = sampler.run(sampler_state, niterations)
>
> This will allow for the most flexibility, I think.
>
> —
> Reply to this email directly or view it on GitHub<https://github.com/choderalab/repex/pull/51/files#r8778693>
> .
>