Constraining bonds that don't include hydrogens

From: Marlon Sidore (
Date: Thu Jan 05 2017 - 08:11:06 CST


Does changing the line, in Molecule.C (as I have seen in the mailing list):
} else if (atoms[atom_number-1].mass <=3.5) {
} else if (atoms[atom_number-1].mass <=3.5 || strcmp(atom_type,"D")==0 ) {
also change anything else but the constraints ?

Does this line mean that, for every atom named "D", the bonds between "D"
and what is bonded to it will be constrained (to the value of the bond
length) ? And is there any other unintended consequences from considering
"D" as a hydrogen ?

Thanks in advance,

Marlon Sidore

PhD Student
Laboratoire d'Ingénierie des Systèmes Macromoléculaire (LISM)
CNRS - UMR7255
31, Chemin Joseph Aiguier
13402 cedex 20 Marseille

This archive was generated by hypermail 2.1.6 : Mon Dec 31 2018 - 23:19:59 CST