Calculate order parameters for lipids in planar membranes.

order out <filename> [x|y|z] [scd] [unsat <mask>][taildist <filename> [delta <resolution>] tailstart <mask> tailend <mask>] <mask0> ... <maskN>

out Output file for order parameters: Sx, Sy, Sz (each succeeded by the standard deviation), and two estimates for the deuterium-order parameter |SCD| = 0.5Sz and |SCD| = -(2Sx + Sy)/3. If scd is set then the order parameter directly computed from the C-H vectors is output.
x|y|z Reference axis. (z)
unsat Mask for unsaturated bonds. Sz is calculated for vector Cn-Cn+1. This is only relevant if scd (below) is not set, i.e. order parameters are calculated from carbon position only.
scd Calculate the deuterium-order parameter |SCD| directly from the C-H vectors (masks must contain C-H-H triplets, see below). Otherwise the order parameter is estimated from carbon positions only (masks must contain only relevant carbons). (false)
taildist Optional output file for end-to-end distances.
delta Optional resolution for taildist. (0.1)
tailstart Mask for the start of the tail. Must be given if taildist.
tailend Mask for the end of the tail. Must be given if taildist.
mask0 ... maskN Masks for each group in the lipid chain.

The order parameters Sx, Sy, Sz and |SCD| are calculated.
Carbons must be given in bonding order. If scd the masks must be made up of C-H-H triples, hence hydrogens to double bonds must be enumerated twice while methyl groups require an additional mask which will also create two entries in the output.

Szis the vector joining carbons Cn-1 and Cn+1, Sx the vector normal to the Cn-1 – Cn and Cn – Cn+1 plane and Sy is the third axis in the molecular coordinate system. The order parameter is then calculated from Sc = 0:5 < 3cos(2q) > -1, where q is the angle to the chosen reference axis. See example input file.

Example input (all atom names according to CHARMM27 force field for POPC). sn1 chain: order parameters Sx, Sy, Sz and jSCDj = 0:5Sz and |SCD| = (2Sx+Sy)/3

lipidorder out sn1.dat z taildist e2e_sn1.dat delta 0.1 \
 tailstart ":POPC@C32" tailend ":POPC@C316" \
 ":POPC@C32" ":POPC@C33" ":POPC@C34" ":POPC@C35" \
 ":POPC@C36" ":POPC@C37" ":POPC@C38" ":POPC@C39" \
 ":POPC@C310" ":POPC@C311" ":POPC@C312" ":POPC@C313" \
 ":POPC@C314" ":POPC@C315" ":POPC@C316"

See also $AMBERHOME/AmberTools/test/cpptraj/Test_LipidOrder.