[gmx-users] mdp-settings for charmm36 and lipid apl values

Justin Lemkul jalemkul at vt.edu
Wed Jun 6 01:08:58 CEST 2018

On 6/5/18 1:03 PM, Muthukumaran Rajagopalan wrote:
> Dear Gromacs Users,
> I have recently started performing membrane simulations in gromacs 5.01 version, I have started running simulations with pure POPE bilayer constructed from charmm-gui membrane builder with XY dimension 70 angs (84 lipids in each bilayer). The bilayer is solvated with 0.15 mol of KCL ( as Na ions have problem with lipid layers). The lipid layer is solvated with hydration number of 36 (lipid:water ratio).
> I went through a series of literature and gromacs mailing list regarding decrease in area per lipid and tried different combinations but the area per lipid decreases by 3-4 angs from the experimental values (~58 for POPE).
> I have referred Pluhackova, K et al J. Phys. Chem. B 2016, 120, 3888−3903

The APL value they obtained was 55.5 A^2, so your observations are 
consistent. The force field apparently underestimates APL slightly.



Justin A. Lemkul, Ph.D.
Assistant Professor
Virginia Tech Department of Biochemistry

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