[gmx-users] Relative Constraints on atoms

Mark Abraham Mark.Abraham at anu.edu.au
Sun Feb 4 00:52:32 CET 2007

Robert Johnson wrote:
> You can apply a harmonic bond between the two atoms.

More precisely, you should apply harmonic distance restraints. While an 
harmonic bond is possible, you want an interaction that does not affect 
the construction of non-bonded exclusion lists. It should be 
straightforward to conserve an alpha helix with some 
thoughtfully-selected pseudo-hydrogen-bonds.

Srinivas refers to position restraints, but there are all manner of 
other restraints that you can read about in the manual.


> 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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