From 13d5deffcce2f56a1c66506ab2b633e00eddedcf Mon Sep 17 00:00:00 2001 From: Siva Dasetty Date: Thu, 20 Jul 2023 10:02:07 -0500 Subject: [PATCH] edits to parameters notes --- parameters.md | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/parameters.md b/parameters.md index 034d00e..80796ce 100644 --- a/parameters.md +++ b/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)