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Coarse-grained bond and angle distributions from atomistic simulations: On the systematic parameterisation of lipid models

Artikel i vetenskaplig tidskrift
Författare Samuel Genheden
Publicerad i Journal of Molecular Graphics and Modelling
Volym 63
Sidor 57–64
ISSN 1093-3263
Publiceringsår 2016
Publicerad vid Institutionen för kemi och molekylärbiologi
Sidor 57–64
Språk en
Länkar dx.doi.org/10.1016/j.jmgm.2015.11.0...
Ämnesord Coarse-graining, Force fields, Parameterisation, Membrane simulations, Martini, Elba
Ämneskategorier Biofysikalisk kemi, Teoretisk kemi

Sammanfattning

Coarse-grained (CG) models are popular alternatives to atomistic (AT) force fields as they enable simulations of larger systems at longer timescales. The bottom-up approach is a systematic parameterisation strategy whereby data from AT simulations are used to determine the CG parameters. This is particular straightforward with the bond and angle parameters as a direct Boltzmann inversion can be used. Still, a reference AT force field has to be chosen. In this study, I compare three common AT force fields (Stockholm lipids, Berger and Gromos) and investigate the sampling of bond and angle distributions in two CG models (Martini and Elba). As a test case, I choose a bilayer of POPC lipids. The AT simulations give distributions that agree to a large extent, especially in the fatty acid tails. However, the AT simulations sample distributions that differ from the distributions observed in CG simulations with respect to both location and width. The bond and angle distributions from the AT simulations are then used to re-parameterise the CG force fields. For the Martini model, this significantly alters the physical behaviour of the membrane, which likely is an effect of the mapping. However, for the Elba model the re-parameterised force field gives a membrane that is in some respects closer to the experimental membrane. Implications for CG parameterisation are discussed.

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