ah I think I understand what you want. it's not a half harmonic, it's
something where only one atom feels the force and the other doesn't. I
think this violates the 3rd law, but you could do it in a simulation. I am
not sure there is any way already set up though. you would probably need to
go into the restraint force calculation and just zero out the contribution
(or not add it) for one of the atoms.
On Tue, Mar 21, 2023 at 4:32 PM Jose Luis Guerra <jlguerra.uchicago.edu>
wrote:
> Thanks Carlos!
>
> To clarify: Right now, I have case 1 where I am trying to keep a molecule
> within a region and force is applied to both atoms. In case 2, I would like
> to keep atom1 unperturbed by the atom that is being pushed back into the
> region.
>
> Case 1: before 0=======0
> after 0=0
> Case 2:before|======0
> after |=0
>
> Thanks again!
>
> Jose
>
> ------------------------------
> *From:* Carlos Simmerling <carlos.simmerling.gmail.com>
> *Sent:* Tuesday, March 21, 2023 1:59 PM
> *To:* Jose Luis Guerra <jlguerra.uchicago.edu>; AMBER Mailing List <
> amber.ambermd.org>
> *Subject:* Re: [AMBER] Half-harmonic restraint
>
> Hi Jose,
> yes you can do this by setting the force constant on one side to be zero.
> Amber lets you set each side of the harmonic separately using rk2 and rk3.
> carlos
>
> On Tue, Mar 21, 2023 at 2:10 PM Jose Luis Guerra via AMBER <
> amber.ambermd.org> wrote:
>
> Hi,
>
> I am wondering if there is a way to implement a half-harmonic restraint on
> a distance between two atoms? (I want the atom of choice to be able to move
> around; I do not have to set a positional restraint).
>
> Best,
>
> Jose Guerra
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Received on Tue Mar 21 2023 - 14:30:02 PDT
