AI Article Synopsis
- Coarse-grained simulation methods are popular due to their ability to significantly speed up molecular simulations, allowing researchers to explore larger time and size scales.
- A new set of parameters and simplified lipid representations compatible with the SIRAH force field has been presented, successfully reproducing key structural and dynamic properties of lipids.
- Incorporating phospholipid membranes into the existing SIRAH force field enables more comprehensive studies of common issues in biomolecular simulations involving proteins and DNA.
Article Abstract
Coarse-grained simulation schemes are increasingly gaining popularity in the scientific community because of the significant speed up granted, allowing a considerable expansion of the accessible time and size scales accessible to molecular simulations. However, the number of compatible force fields capable of representing ensembles containing different molecular species (i.e., Protein, DNA, etc) is still limited. Here, we present a set of parameters and simplified representation for lipids compatible with the SIRAH force field for coarse-grained simulations ( http://www.sirahff.com ). We show that the present model not only achieves a correct reproduction of structural parameters as area per lipid and thickness, but also dynamic descriptors such as diffusion coefficient, order parameters, and proper temperature driven variations. Adding phospholipid membranes to the existing aqueous solution, protein and DNA representations of the SIRAH force field permit considering the most common problems tackled by the biomolecular simulation community.
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| http://dx.doi.org/10.1007/s00894-017-3426-5 | DOI Listing |
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