Collective Motion Artifacts Arising in Long-Duration Molecular Dynamics Simulations

See Wing Chiu, Michael Clark, Shankar Subramaniam, Eric Jakobsson

Research output: Contribution to journalArticle

Abstract

We tested a variety of molecular dynamics simulation strategies in long-duration (up to several nanoseconds) constant-temperature simulations of liquid water under periodic boundary conditions. Such long durations are necessary to achieve adequate conformational sampling in simulations of membrane assemblies and other large biomolecular systems. Under a variety of circumstances, serious artifacts arise in the form of spurious collective behavior that becomes obvious only after the simulation has gone at least several hundred picoseconds. The potential energy of the system drops and the system changes from a liquid to an icy or glassy state. The underlying cause is accumulated center-of-mass motion of the system, coupled with velocity rescaling associated with constant-temperature control. The velocity rescaling in the constant-temperature algorithm reduces the thermal velocity as the net center-of-mass velocity grows, effectively causing the kinetic energy of the system to drain from thermal motions into coordinated motions. We found that the incidence and magnitude of the underlying artifactual motion leading to the spurious transition is mediated by: choice of method for computing electrostatic interactions; choice of ensemble; size of the simulation cell; SHAKE tolerance; frequency of nonbonded pairlist updating; and closeness of coupling to the temperature bath. The appearance of the spurious transition can be avoided by periodically subtracting net center-of-mass motion during the dynamics, or by improving the accuracy of the simulation by means of tightening SHAKE tolerance and updating nonbonded pairlists every timestep.

Original languageEnglish (US)
Pages (from-to)121-131
Number of pages11
JournalJournal of Computational Chemistry
Volume21
Issue number2
DOIs
StatePublished - Jan 30 2000

Keywords

  • Computational artifacts
  • Ewald sums
  • Molecular dynamics
  • Simulation methods
  • Water simulations

ASJC Scopus subject areas

  • Chemistry(all)
  • Computational Mathematics

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