Display options
Cite
Loubet B, Kopec W, Khandelia H. Accelerating All-Atom MD Simulations of Lipids Using a Modified Virtual-Sites Technique. J Chem Theory Comput. 2014;10(12):5690-5doi: 10.1021/ct500100f.
Loubet, B., Kopec, W., & Khandelia, H. (2014). Accelerating All-Atom MD Simulations of Lipids Using a Modified Virtual-Sites Technique. Journal of chemical theory and computation, 10(12), 5690-5. https://doi.org/10.1021/ct500100f
Loubet, Bastien, et al. "Accelerating All-Atom MD Simulations of Lipids Using a Modified Virtual-Sites Technique." Journal of chemical theory and computation vol. 10,12 (2014): 5690-5. doi: https://doi.org/10.1021/ct500100f
Loubet B, Kopec W, Khandelia H. Accelerating All-Atom MD Simulations of Lipids Using a Modified Virtual-Sites Technique. J Chem Theory Comput. 2014 Dec 09;10(12):5690-5. doi: 10.1021/ct500100f. PMID: 26583251.
Copy Download .nbib Format: NLM
Share it on

J Chem Theory Comput. 2014 Dec 09;10(12):5690-5. doi: 10.1021/ct500100f.

Accelerating All-Atom MD Simulations of Lipids Using a Modified Virtual-Sites Technique.

Journal of chemical theory and computation

Bastien Loubet, Wojciech Kopec, Himanshu Khandelia

Affiliations

  1. MEMPHYS - Center for Biomembrane Physics, Department of Physics, Chemistry and Pharmacy, University of Southern Denmark , Campusvej 55, 5230 Odense M, Denmark.

PMID: 26583251 DOI: 10.1021/ct500100f

Abstract

We present two new implementations of the virtual sites technique which completely suppresses the degrees of freedom of the hydrogen atoms in a lipid bilayer allowing for an increased time step of 5 fs in all-atom simulations of the CHARMM36 force field. One of our approaches uses the derivation of the virtual sites used in GROMACS while the other uses a new definition of the virtual sites of the CH2 groups. Our methods is tested on a DPPC (no unsaturated chain), a POPC (one unsaturated chain), and a DOPC (two unsaturated chains) lipid bilayers. We calculate various physical properties of the membrane of our simulations with and without virtual sites and explain the differences and similarity observed. The best agreements are obtained for the GROMACS original virtual sites on the DOPC bilayer where we get an area per lipid of 67.3 ± 0.3 Å(2) without virtual sites and 67.6 ± 0.3 Å(2) with virtual sites. In conclusion the virtual-sites technique on lipid membranes is a powerful simulation tool, but it should be used with care. The procedure can be applied to other force fields and lipids in a straightforward manner.

Publication Types