Mods input file

The mods input specifies which atomistic properties should be modified during a ThermoDiff run. Each modification requires a separate set of reruns, and can encompass any set of atoms (see below), from a single atom in a single residue to a specific group of atoms in all given residues to all atoms bearing a specified type.

ThermoDiff then calculates how the particular quantity (free energies, ensemble averaves, profiles etc.) respond to a change in the given atomistic property.

Note that many lines can be contained in a single input file, each input letter ([cseadnm]) corresponding to a new set of reruns:

  • c corresponds to a change in charge
  • s corresponds to a change in \(\sigma\)
  • e corresponds to a change in \(\varepsilon\)
  • a corresponds to a change in angle force constant
  • d corresponds to a change in dihedral force constant
  • n corresponds to a change in pairwise \(\sigma\) (NBFIX)
  • m corresponds to a change in pairwise \(\varepsilon\) (NBFIX)

Sample input lines

Modify charge/\(\sigma\)/\(\varepsilon\)

  • chosen atoms of a single type, all within a single residue (note: need to be of the same type):
cse AMFB-1 O11 O12 O13 O6 O7 O9 O10 O1 O2 O16
  • chosen atoms of a single type, possibly different residues (note: need to be of the same type):
cse AMFB-1-O11 AMFB-1-O12 AMFB-1-O13 AMFB-1-O6 AMFB-1-O7 AMFB-1-O9
  • all atoms of a specified type:
cse OG311

Modify angle/dihedral parameters

  • chosen sets of atoms, all within a single residue (possible multiples of 3 (angles) or 4 (dihedrals) in a single line):
d AMFB-1 C1 C2 C3 C4
a AMFB-1 C1 C2 C3 C1 C2 C4
  • chosen sets of atoms, possibly different residues (note: need to have the same type signature):
d AMFB-1-C1 AMFB-1-C2 AMFB-1-C3 AMFB-1-C4
a AMFB-1-C1 AMFB-1-C2 AMFB-1-C3 AMFB-1-C1 AMFB-1-C2 AMFB-1-C4
  • chosen set of types:
a CG311 CG311 OG311
d OG311 CG311 CG311 OG311

Modify nbfix \(\sigma\)/\(\varepsilon\)

  • chosen sets of atoms, all within a single residue (“;”-delimited; here O11, O12 and O13 need to have consistent types, as well as H1, H2 and H3)
nm AMFB-1 O11 O12 O13; H1 H2 H3
  • chosen sets of atoms, possibly different residues (“;”-delimited; need to have consistent types, as above)
nm AMFB-1-O11 AMFB-1-O12 AMFB-1-O13; AMFB-1-H1 AMFB-1-H2 AMFB-1-H3
  • chosen pair of types:
nm HGA2 OG311

Note that ‘n’ refers to NBFIX-\(\sigma\) and ‘m’ refers to NBFIX-\(\varepsilon\); other cases should be intuitive (‘c’ for charge, ‘s’ for sigma etc.)