Giacomo Bastianelli wrote:
I tried to include the distance contraints in my .top file as follows:
Distance "restraints" are what you want, not "constraints". Read 4.3.4
in the manual.
Notwithstanding, the stuff below should work so long as your constrained
atoms are in the same molecule, you've put the [ constraints ] directive
in the right position with respect to the [ molecule ] directive, the
molecule is correctly defined, and the starting geometry is not too far
from the constrained distance.
[ constraints ]
; atom1 atom2 function distance
1 245 2 0.133
this is my output:
Fatal error:
[ file "1NB1.top", line 1665 ]:
Atom index (245) in constraints out of bounds (1-1)
grompp thinks the molecule to which you are applying constraints has
only 1 atom (hence 1-1). Probably you've #included some ion just before
this, and thus have your [ constraints ] directive associated with the
wrong [ molecule ] directive, or made some catastrophic error with your
topology.
I thought that the function number 2 would have not create
the bond between the two atoms but just constrained the distance.
Yes.
Mark
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