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.
Mark
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