[gmx-users] Relative Constraints on atoms

[Srinivas Ramachandran]

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