Merge pull request #15 from Ferg-Lab/sd_edits

edits to parameters notes

parameters.md

@@ -35,7 +35,7 @@ Label for referencing this module elsewhere in the PLUMED file.
 
 - PINESATOMS: Total number of atom types. This is the same as the length of ATOMTYPES and is used for detecting errors in ATOMTYPES declaration.
 
-- ATOMTYPES: All atomtypes of solute + solvent for defining the blocks in PIV. In the ONLYCROSS case, the order of the final PIV is based on the sequence of the atom types defined here. In brief, the order of PIV is solute1-solute2, solute1-solute3, ..., solute1-soluteN, solute1-OW [of size equal to NL_CONSTANT_SIZE defined below], solute1-H1 [of size equal to NL_CONSTANT_SIZE defined below], solute2-solute3, solute2-solute4, ..., solute2-soluteN, solute2-OW [of size equal to NL_CONSTANT_SIZE defined below], solute2-H1 [of size equal to NL_CONSTANT_SIZE defined below], ..., soluteN-OW [of size equal to NL_CONSTANT_SIZE defined below], soluteN-H1 [of size equal to NL_CONSTANT_SIZE defined below]. The oxygen atoms are extracted based on NL_CUTOFF and only the number of oxygen atoms equal to NL_CONSTANT_SIZE are retained. Similarly, hydrogen atoms are extracted based on atom indices that share the residue numbers with the oxygen atom indices and only NL_CONSTANT_SIZE hydrogen atoms are retained. Consequently, the total number of elements in PIV is equal to (PINESATOMS-3)x(PINESATOMS-3)x0.5 + (PINESATOMS-3)xNL_CONSTANT_SIZE + (PINESATOMS-3)xNL_CONSTANT_SIZE. The number of blocks is (PINESATOMS-3)x(PINESATOMS-3)x0.5 + (PINESATOMS-3) + (PINESATOMS-3)
+- ATOMTYPES: All atomtypes of solute + solvent for defining the blocks in PIV. In the ONLYCROSS case, the order of the final PIV is based on the sequence of the atom types defined here. In brief, the order of PIV is solute1-solute2, solute1-solute3, ..., solute1-soluteN, solute1-OW [of size equal to NL_CONSTANT_SIZE defined below], solute1-H1 [of size equal to NL_CONSTANT_SIZE defined below], solute2-solute3, solute2-solute4, ..., solute2-soluteN, solute2-OW [of size equal to NL_CONSTANT_SIZE defined below], solute2-H1 [of size equal to NL_CONSTANT_SIZE defined below], ..., soluteN-OW [of size equal to NL_CONSTANT_SIZE defined below], soluteN-H1 [of size equal to NL_CONSTANT_SIZE defined below]. The oxygen atoms are extracted based on NL_CUTOFF and only the number of oxygen atoms equal to NL_CONSTANT_SIZE are retained. Similarly, hydrogen atoms are extracted based on atom indices that share the residue numbers with the oxygen atom indices and only NL_CONSTANT_SIZE hydrogen atoms are retained. Consequently, the total number of elements in PIV is equal to (PINESATOMS-3)x(PINESATOMS-3)x0.5 + (PINESATOMS-3)xNL_CONSTANT_SIZE + 2x(PINESATOMS-3)xNL_CONSTANT_SIZE. The number of blocks is (PINESATOMS-3)x(PINESATOMS-3)x0.5 + (PINESATOMS-3) + (PINESATOMS-3)
 
 - SFACTOR: Should be the same size as of nblocks = (PINESATOMS-3)x(PINESATOMS-3)x0.5 + (PINESATOMS-3) + (PINESATOMS-3)