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. Author manuscript; available in PMC: 2015 Jun 29.
Published in final edited form as: Methods Mol Biol. 2015;1273:391–406. doi: 10.1007/978-1-4939-2343-4_24

Table 2.

Various force constants during the equilibration steps.

step 4.1 4.2 4.3 4.4 4.5 4.6 4.7 4.8 4.9 4.10
kwater1 2.5 2.5 1 1 0.5 0.1 0 0 0 0
khead2 2.5 2.5 1 1 0.5 0.1 0 0 0 0
ktail3 2.5 2.5 1 1 0.5 0.1 0 0 0 0
kchiral4 250 100 50 50 25 5 0 0 0 0
kring5 250 200 150 100 100 50 50 50 25 25
kbilayer6 0 0 0 0 0 0 1 1 1 1
1

kwater is the force constant [in kcal/(mol·Å2)] for the repulsive planar restraints to prevent water from entering into the membrane hydrophobic region (|Z| < 12 Å).

2

khead is the force constant [in kcal/(mol·Å2)] for the planar restraints to hold the position of lipid A PA and PB along the Z-axis (Z = 20 Å for the upper leaflet and Z = −20 Å for the lower leaflet).

3

ktail is the force constant [in kcal/(mol·Å2)] for the planar restraints to keep the last atoms of lipid A acyl chains in (|Z| < 5 Å).

4

kchiral is the force constant [in kcal/(mol·rad2)] for the dihedral restraints to maintain the correct chirality in the lipid A.

5

kring is the force constant [in kcal/(mol·rad2)] for the dihedral restraints to maintain the chair conformation of sugars.

6

kbilayer is the force constant [in kcal/(mol·Å2)] for the planar restraint to hold the position of lipid A molecules at Z = 0.