GAFFlipid: a General Amber Force Field for the accurate molecular dynamics simulation of phospholipid
Previous attempts to simulate phospholipid bilayers using the General Amber Force Field (GAFF) yielded many bilayer characteristics in agreement with experiment, however when using a tensionless NPT ensemble the bilayer is seen to compress to an undesirable extent resulting in low areas per lipid an...
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| Published in | Soft matter Vol. 8; no. 37; pp. 9617 - 9627 |
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| Main Authors | , , , , |
| Format | Journal Article |
| Language | English |
| Published |
01.01.2012
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| Subjects | |
| Online Access | Get full text |
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| Abstract | Previous attempts to simulate phospholipid bilayers using the General Amber Force Field (GAFF) yielded many bilayer characteristics in agreement with experiment, however when using a tensionless NPT ensemble the bilayer is seen to compress to an undesirable extent resulting in low areas per lipid and high order parameters in comparison to experiment. In this work, the GAFF Lennard-Jones parameters for the simulation of acyl chains are corrected to allow the accurate and stable simulation of pure lipid bilayers. Lipid bilayers comprised of six phospholipid types were simulated for timescales approaching a quarter of a microsecond under tensionless constant pressure conditions using Graphics Processing Units. Structural properties including area per lipid, volume per lipid, bilayer thickness, order parameter and headgroup hydration show favourable agreement with available experimental values. Expanding the system size from 72 to 288 lipids and a more experimentally realistic 2 288 lipid bilayer stack induces little change in the observed properties. This preliminary work is intended for combination with the new AMBER Lipid11 modular force field as part of on-going attempts to create a modular phospholipid AMBER force field allowing tensionless NPT simulations of complex lipid bilayers. |
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| AbstractList | Previous attempts to simulate phospholipid bilayers using the General Amber Force Field (GAFF) yielded many bilayer characteristics in agreement with experiment, however when using a tensionless NPT ensemble the bilayer is seen to compress to an undesirable extent resulting in low areas per lipid and high order parameters in comparison to experiment. In this work, the GAFF Lennard-Jones parameters for the simulation of acyl chains are corrected to allow the accurate and stable simulation of pure lipid bilayers. Lipid bilayers comprised of six phospholipid types were simulated for timescales approaching a quarter of a microsecond under tensionless constant pressure conditions using Graphics Processing Units. Structural properties including area per lipid, volume per lipid, bilayer thickness, order parameter and headgroup hydration show favourable agreement with available experimental values. Expanding the system size from 72 to 288 lipids and a more experimentally realistic 2 288 lipid bilayer stack induces little change in the observed properties. This preliminary work is intended for combination with the new AMBER Lipid11 modular force field as part of on-going attempts to create a modular phospholipid AMBER force field allowing tensionless NPT simulations of complex lipid bilayers. |
| Author | Dickson, Callum J. Rosso, Lula Betz, Robin M. Walker, Ross C. Gould, Ian R. |
| Author_xml | – sequence: 1 givenname: Callum J. surname: Dickson fullname: Dickson, Callum J. – sequence: 2 givenname: Lula surname: Rosso fullname: Rosso, Lula – sequence: 3 givenname: Robin M. surname: Betz fullname: Betz, Robin M. – sequence: 4 givenname: Ross C. surname: Walker fullname: Walker, Ross C. – sequence: 5 givenname: Ian R. surname: Gould fullname: Gould, Ian R. |
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