Studying equilibria of polymers in solution by direct molecular dynamics simulations: poly(N-isopropylacrylamide) in water as a test case
Laboratory of Engineering Thermodynamics (LTD), University of Kaiserslautern, Erwin-Schrödinger-Str. 44, 67663, Kaiserslautern, Germany
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Received in final form: 27 November 2018
Published online: 8 March 2019
It is well known that studying equilibria of polymers in solution by atomistic simulations is computationally demanding as a large phase space has to be adequately sampled. Nevertheless, direct molecular dynamics (MD) simulations are often used for this purpose in the literature. To assess whether such approach is adequate, we have conducted a case study for a polymer + solvent system that has been commonly studied with direct MD simulations by many authors: poly(N-isopropylacrylamide) (PNIPAM) in water. The total simulation time of the present study is much longer than that typically used in MD simulations of that system. A NIPAM chain of 30 monomers was studied in explicit water at 295 K. Three initial configurations were used. For each configuration, five replicas were run for 1000 ns. The statistical analysis of our data shows that the equilibration time is of the order of 600–700 ns and that the remaining time for the production run is not sufficient to sample the equilibrium state adequately. These results underpin the well-known difficulty of sampling equilibrium states of polymers in solution with direct MD simulations and the need for a careful interpretation of results of such studies. The problem with the unsatisfactory sampling persists despite the increasing available computing power. Therefore, enhanced sampling techniques and workarounds, such as simplified scenarios or coarse-graining, remain important.
© EDP Sciences, Springer-Verlag GmbH Germany, part of Springer Nature, 2019