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ReplicaExchangeSampler test code fails
Hi, I tried to run the test code shown in ReplicaExchangeSampler documentation.
#!/usr/bin/env python
import math
from simtk import unit
from openmmtools import testsystems, states, mcmc, multistate
testsystem = testsystems.AlanineDipeptideImplicit()
import os
import tempfile
n_replicas = 3
T_min = 298.0 * unit.kelvin
T_max = 600.0 * unit.kelvin
temperature = [T_min + (T_max-T_min) * (math.exp(float(i) / float(n_replicas-1))-1.0) / (math.e - 1.0) for i in range(n_replicas)]
thermodynamic_states = [states.ThermodynamicState(system=testsystem.system, temperature=T) for T in temperature]
move = mcmc.GHMCMove(timestep=2.0*unit.femtoseconds, n_steps=50)
simulation = multistate.ReplicaExchangeSampler(mcmc_moves=move, number_of_iterations=2)
reporter = multistate.MultiStateReporter('test.nc',checkpoint_interval=1)
simulation.create(thermodynamic_states=thermodynamic_states,
sampler_states=states.SamplerState(testsystem.positions),
storage=reporter)
simulation.run()
print(simulation.iteration)
simulation.run(n_iterations=1)
print(simulation.iteration)
This is the output
Warning: The openmmtools.multistate API is experimental and may change in future releases
Warning: The openmmtools.multistate API is experimental and may change in future releases
Please cite the following:
Friedrichs MS, Eastman P, Vaidyanathan V, Houston M, LeGrand S, Beberg AL, Ensign DL, Bruns CM, and Pande VS. Accelerating molecular dynamic simulations on graphics processing unit. J. Comput. Chem. 30:864, 2009. DOI: 10.1002/jcc.21209
Eastman P and Pande VS. OpenMM: A hardware-independent framework for molecular simulations. Comput. Sci. Eng. 12:34, 2010. DOI: 10.1109/MCSE.2010.27
Eastman P and Pande VS. Efficient nonbonded interactions for molecular dynamics on a graphics processing unit. J. Comput. Chem. 31:1268, 2010. DOI: 10.1002/jcc.21413
Eastman P and Pande VS. Constant constraint matrix approximation: A robust, parallelizable constraint method for molecular simulations. J. Chem. Theor. Comput. 6:434, 2010. DOI: 10.1021/ct900463w
Chodera JD and Shirts MR. Replica exchange and expanded ensemble simulations as Gibbs multistate: Simple improvements for enhanced mixing. J. Chem. Phys., 135:194110, 2011. DOI:10.1063/1.3660669
python(69740,0x11999fdc0) malloc: *** error for object 0x7ff60b6e1eb8: pointer being freed was not allocated
python(69740,0x11999fdc0) malloc: *** set a breakpoint in malloc_error_break to debug
The environment is MacOS 10.15.5 Catalina Python 3.7.4 (Clang 4.0.1 Anaconda) openmmtools 0.20.0 py37_0 omnia