# Re: [AMBER] Distance restraints

From: Carlos Simmerling via AMBER <amber.ambermd.org>
Date: Tue, 10 Jan 2023 08:58:09 -0400

Yes that's right, though you could simplify by using the atom numbers in
the iat= instead of - 1. Using - 1 indicates a center of mass of the atoms
in igr, but since you only have one atom you cna just specify it directly
with iat=15,59. I hope that's clear.

On Tue, Jan 10, 2023, 4:58 AM Juliette Newell via AMBER <amber.ambermd.org>
wrote:

> Dear Amber community,
>
> I am struggling with applying distance restraints to my system
> I have dist.dat file similar to:
>
> &rst iat =-1,-1, igr1 = 15, igr2 = 59,
> r1 = 0, r2 = 95, r3 = 95, r4 = 105, rk2 = 0.001, rk3 =3,
> r1a = 0, r2a = 95, r3a = 95, r4a = 105, rk2a = 0.001, rk3a =3
>
> I think I am applying a distance restraint between atom 15 and 59, and as
> the atoms aproach a distance of 0 this has a corresponding force constant
> of 0.001, and as the atoms disperse to a distance of 105 this has a force
> constant of 3. This should mean at small distances there is little
> restraint allowing the atoms to get closer together, and at larger
> distances there is a larger restraint preventing the atoms from dispersing
> too much? Is someone please able to clarify that I have the right inputs
> in mt dist.dat file?
>
> Thank you,
> Juliette
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Received on Tue Jan 10 2023 - 05:00:03 PST
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