calc mxa @NL * 6 * 4
calc mxs 10 + @NL*2 * 4
calc mxt 500 * @N
These lines compute the values needed for CORREL startup, i.e. MAXAtoms, MAXSeries, and MAXTimesteps; their meaning is described in correl.doc
The value '500' may need to be changed, as it is based on the number of stored coordinate sets in each trajectory file. The variable @NL is the number of lipid molecules, and is set near the top of the main script.
if c gt 15 goto eskip
if ug eq 0 then
The above two lines are exception code added specifically for POPC, where the gamma chain (a.k.a. chain 1) has only 16 C atoms.
define unsat sele atom D 1 C2@C .and. chem CEL1 end
what is the meaning of 1, chem and CEL1?
Another atom selection issue (select.doc); the CHEM token allows one to select atoms based on their parameter type, rather than a IUPAC style label. The CEL1 parameter type is specific for a C atom involved in a C=C double bond.
