[gmx-users] Relative Constraints on atoms
bobjohnson1981 at gmail.com
Sun Feb 4 01:05:53 CET 2007
Will function type 5 or 6 (for the harmonic bond) affect the
non-bonded exclusion list?
On 2/3/07, Mark Abraham <Mark.Abraham at anu.edu.au> wrote:
> 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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