Behavior of [link] terms spanning 3 residues

[ricalessandri]

Gonna try the discussions :)

Weird behavior - at least for me - observed when having links spanning 3 residues. Namely, seemingly equivalent lines would give different behaviors.

Namely, the following 2 combinations would work as expected, i.e., print those "i-j-k" terms when needed (i.e., at least 3 residues present):

[link]
resname "PMMA"
[ dihedrals ]
++C01  +C02  +C01   C02     3      2.301     -1.464      0.837     -1.674     -0.000      0.000   {"comment":"i-j-k", "group":"connection"}
[ pairs ]
  C02  ++C01       1   {"comment":"i-j-k", "group":"connection"}

[link]
resname "PMMA"
[ dihedrals ]
+C01   C02   C01  -C02     3      2.301     -1.464      0.837     -1.674     -0.000      0.000   {"comment":"i-j-k", "group":"connection"}
[ pairs ]
-C02   +C01       1   {"comment":"i-j-k", "group":"connection"}

While the following combinations will not print these terms in the itp:

[link]
resname "PMMA"
[ dihedrals ]
 +C01   C02   C01  -C02     3      2.301     -1.464      0.837     -1.674     -0.000      0.000   {"comment":"i-j-k", "group":"connection"}
[ pairs ]
  C02  ++C01       1   {"comment":"i-j-k", "group":"connection"}

[link]
resname "PMMA"
[ dihedrals ]
 ++C01  +C02  +C01   C02     3      2.301     -1.464      0.837     -1.674     -0.000      0.000   {"comment":"i-j-k", "group":"connection"}
[ pairs ]
 -C02   +C01       1   {"comment":"i-j-k", "group":"connection"}

or maybe I'm missing something and this is intended (for some good reason)?

[fgrunewald]

@ricalessandri the problem here is the pair directive which in the last two examples has a prefix that does not occur in dihedrals so it actually requires 5 residues not 4

[ricalessandri]

@fgrunewald you mean 4 residues instead of 3, right? (- = residue 1, = residue 2, + = residue 3, ++ = residue 4)

OK, so that means that a link cannot span more than 3 residues?

[fgrunewald]

My bad my math was off: Case 1 & 2 span 3 residues, but case 3 & 4 span 4 residues, so they are not equivalent. Plus pairs don't make edges, which means that you have a disconnected residue in case 3&4. You need to edges between the correct atoms in the link.

[fgrunewald]

Nice use of the discussion feature by the way!