Comparison of Molecular Dynamics with Hybrid Continuum-Molecular Dynamics for a Single Tethered Polymer in a Solvent

Details Comparison of Molecular Dynamics with Hybrid Continuum-Molecular Dynamics for a Single Tethered Polymer in a Solvent Comparison of Molecular Dynamics with Hybrid Continuum-Molecular Dynamics for a Single Tethered Polymer in a Solvent

2004-01-21

arxiv.org/abs/cond-mat/0401392v2

Physics

Condensed Matter

Soft Condensed Matter

13 pages, 8 figures

Scientific paper

10.1063/1.1767996

We compare a newly developed hybrid simulation method which combines classical molecular dynamics (MD) and computational fluid dynamics (CFD) to a simulation consisting only of molecular dynamics. The hybrid code is composed of three regions: a classical MD region, a continuum domain where the dynamical equations are solved by standard CFD methods, and an overlap domain where transport information from the other two domains is exchanged. The exchange of information in the overlap region ensures that momentum, energy and mass are conserved. The validity of the hybrid code is demonstrated by studying a single polymer tethered to a hard wall immersed in explicit solvent and undergoing shear flow. In classical molecular dynamics simulation a great deal of computational time is devoted to simulating solvent molecules, although the solvent itself is of no direct interest. By contrast, the hybrid code simulates the polymer and surrounding solvent explicitly, whereas the solvent farther away from the polymer is modeled using a continuum description. In the hybrid simulations the MD domain is an open system whose number of particles is controlled to filter the perturbative density waves produced by the polymer motion.We compare conformational properties of the polymer in both simulations for various shear rates. In all cases polymer properties compare extremely well between the two simulation scenarios, thereby demonstrating that this hybrid method is a useful way to model a system with polymers and under nonzero flow conditions. There is also good agreement between the MD and hybrid schemes and experimental data on tethered DNA in flow. The computational cost of the hybrid protocol can be reduced to less than 6% of the cost of updating the MD forces, confirming the practical value of the method.

Affiliated with

Also associated with

No associations

Rating

Comparison of Molecular Dynamics with Hybrid Continuum-Molecular Dynamics for a Single Tethered Polymer in a Solvent does not yet have a rating. At this time, there are no reviews or comments for this scientific paper.

If you have personal experience with Comparison of Molecular Dynamics with Hybrid Continuum-Molecular Dynamics for a Single Tethered Polymer in a Solvent, we encourage you to share that experience with our LandOfFree.com community. Your opinion is very important and Comparison of Molecular Dynamics with Hybrid Continuum-Molecular Dynamics for a Single Tethered Polymer in a Solvent will most certainly appreciate the feedback.

Rate now

Comments { 0 }

Profile ID: LFWR-SCP-O-641425