[gmx-users] mdp-settings for charmm36 and lipid apl values
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.
Virginia Tech Department of Biochemistry
303 Engel Hall
340 West Campus Dr.
Blacksburg, VA 24061
jalemkul at vt.edu | (540) 231-3129
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