[gmx-users] distances between atoms in an electrostatic interaction

Mark Abraham Mark.Abraham at anu.edu.au
Thu May 6 15:51:23 CEST 2010

On 6/05/2010 8:00 PM, abdullah ahmed wrote:
> Dear Gromacs users,
> I have an electrostatic interaction in my structure between GLU and LYS.
> After minimization the distance between the Hydrogen molecule on the
> Lysine and the Oxygen on the GLU is reduced to 1.4 A°.
> *Is it possible to pre-set this distance to be 1.6 A° instead?*
> I realize that using a distance restraint could be one way to do this. I
> would like to know if there is another way to do it that will not affect
> the final toa=tal energy term.

Any way of doing it will affect the energy term, but that energy term 
doesn't mean much of anything anyway.

If your magic distance is from a crystal structure, then you should 
prefer to look at the inter-heavy-atom distances.

If you are comparing apples with apples, then you've demonstrated that 
your model physics is somehow inappropriate. Energy-minimized structures 
need have no correlation to those found at equilibrium.


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