a little right in the idea, but the details here are causing your problem.
a negative force constant will be an inverted parabola, and for the short
distance will become an attraction towards 0. so you don't want that. I
would use a *positive force constant*, but only on the left side of the
parabola so it is repulsive at short distance, and zero force constant for
the right side. this give a half parabola. if you use the value of 13 as in
your sample, it will feel no force until 13A distance, then get repulsive.
that's still long, you might want to use shorter r2 but that depends on the
details of where you do want it to be able to explore.
On Tue, Apr 4, 2023 at 7:33 AM Antonio Frances Monerris via AMBER <
amber.ambermd.org> wrote:
> Dear Amber community,
>
> I am interested in running simulations of a DNA double strand and some
> small drugs. I want to avoid favorable interactions of the drug with the
> DNA terminal base pairs, which have no biological meaning. Therefore, one
> possibility is to add repulsive potentials between these fragments and the
> drug, which are only active at short DNA termninal/drug distances.
>
> I could not find much information about adding repulsive potentials in
> Amber on the internet. I just found in an old Amber post the possibility to
> include negative force constants for an harmonic potential, in the form:
>
> &rst
> iat=1291,20,
> r1=0.0,r2=13.0,r3=13.00,r4=20.0,
> rk2=-65.0, rk3=0.0,
> /
>
>
> This would add a repulsion between atoms 1291 and 20 with a force constant
> of -65 kcal/mol in distances between 0 and 13 Angstrom, and of 0 kcal/mol
> at distances between 13 and 20 Angstrom.
>
> However, this strategy is not working well. In some instances, instead of
> repulsion, the atoms are approaching each other blowing up the simulation.
>
> Am I doing it correctly? Is there any other possibility to avoid these
> undesired contacts?
>
> Thanks for your time.
>
> Best regards,
> Antonio
>
>
>
> --
> ********************************************
>
> Dr. Antonio Francés Monerris
> Assistant Professor
> Institut de Ciència Molecular (ICMol) &
> Departament de Química Física
> Universitat de València
> Phone: +34 963544404
> E-mail: antonio.frances.uv.es
>
> ********************************************
>
>
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>
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Received on Tue Apr 04 2023 - 05:00:02 PDT
