[gmx-users] Relative Constraints on atoms

[Mark Abraham]

Robert Johnson wrote:
> Will function type 5 or 6 (for the harmonic bond) affect the
> non-bonded exclusion list?

5 does, 6 doesn't. Have a look at table 5.4 and sections 4.3.4 and 5.3.5 
in the manual for more info. Actually the manual contradicts my 
suggestion of using distance restraints, but they do offer the advantage 
of being able to have a flat region of zero potential at the bottom of 
the well, so would be ideal for preserving a hydrogen bond over a range 
of acceptable lengths, but only perturbing the potential when necessary.

Mark