My goal is to perturb one thing, fix tests, then repeat.
On Jan 9, 2014 9:14 PM, "Kyle Beauchamp" <kyleabeauchamp@gmail.com> wrote:

> 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>
>> .
>>
>