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Temperature dependent potential #796

@ParivasFeyzishendi

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@ParivasFeyzishendi

Hi,
I'm Parivash Feyzishendi, a 3rd year PhD student. We are dealing with a system where system's potential energy is also temperature dependent. For example, while computing Coulomb potential, the dielectric constant depends on the Temperature. Now if we perform replica exchange on this system, does the metropolis acceptance takes care of this temperature dependence during the swap of conformations?
Looking at the github code, it looks like that for each replica exchange between states i and j, potential energy of each replica is calculated at both temperatures i and j, essentially taking care of the temperature dependence. However, before implementing this in our coarse-grained RNA model system, we wanted to confirm if this is the case? We have highlighted the portion of the code herewith "

# Accept or reject.
if log_p_accept >= 0.0 or np.random.rand() < np.exp(log_p_accept):
# Swap states in replica slots i and j.
_replica_thermodynamic_states[replica_i] = thermodynamic_state_j
_replica_thermodynamic_states[replica_j] = thermodynamic_state_i
# Accumulate statistics.
_n_accepted_matrix[thermodynamic_state_i, thermodynamic_state_j] += 1
_n_accepted_matrix[thermodynamic_state_j, thermodynamic_state_i] += 1
".
thank you so much for your time,
Parivash

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