meld.remd.adaptor

class meld.remd.adaptor.AcceptanceCounter(n_replicas)

Class to keep track of acceptance rates.

class meld.remd.adaptor.AdaptationPolicy(growth_factor, burn_in, adapt_every)

Repeat adaptation on a regular schedule with an optional burn-in and increasing adaptation times.

Parameters:

• growth_factor – increase adapt_every by a factor of growth_factor every adaptation
• burn_in – number of steps to ignore at the beginning
• adapt_every – how frequently to adapt (in picoseconds)

class AdaptationRequired

AdaptationRequired(adapt_now, reset_now)

adapt_now

Alias for field number 0

reset_now

Alias for field number 1

AdaptationPolicy.should_adapt(step)

Is adaptation required?

Parameters:step – the current simulation step Returns:an AdaptationPolicy.AdaptationRequired object indicating if adaptation or resetting is necessary

class meld.remd.adaptor.EqualAcceptanceAdaptor(n_replicas, adaptation_policy, min_acc_prob=0.1)

Adaptor based on making acceptance rates uniform.

Parameters:

• n_replicas – number of replicas
• min_acc_prob – all acceptence probabilities below this value will be raised to this value

adapt(previous_lambdas, step)

Compute new optimal values of lambda.

Parameters:

• previous_lambdas – a list of the previous lambda values
• step – the current simulation step

Returns:

a list of the new, optimized lambda values

reset()

Forget about any previous updates.

Resets all internal counters and statistics to zero.

update(i, accepted)

Update adaptor with exchange.

Parameters:

• i – index of first replica; second replica is i+1
• accepted – True if the exchange was accepted