[gmx-users] Relative Constraints on atoms

[Robert Johnson]

You can apply a harmonic bond between the two atoms.

On 2/3/07, Srinivas Ramachandran <tr.srinivas at gmail.com> wrote:
> Dear all,
>
> I know that we can place harmonic constraints on selective atoms,
> specified by an index file. But this only ensures that the atom
> position remains same throughout the simulation.
>
> But if I only want two atoms' positions to remain same only relative
> to one another but the atoms can move otherwise, is there any way to
> do this? I want to know this because I want a fragment of the protein
> to remain alpha helical throughout the simulation, but I dont want it
> to conserve its original co-ordinates.
>
> Regards
> Srinivas Ramachandran
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