You can apply a harmonic bond between the two atoms.
On 2/3/07, Srinivas Ramachandran <[EMAIL PROTECTED]> 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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