yes negative rk gives an inverted parabola, so it is repulsive if it is
outside the flat region.
did the restraints get properly read?
On Mon, Mar 15, 2021 at 7:28 PM Ming Tang <m21.tang.qut.edu.au> wrote:
> Hi Carlos,
>
> should rk2 be negative when applying repulsive for between two groups
> closer than r2? When I set it to 50, the two groups are close but the
> restrain in output file is 0.
>
> Thanks,
> Ming
>
> -----Original Message-----
> From: Carlos Simmerling <carlos.simmerling.gmail.com>
> Sent: Friday, 26 February 2021 3:02 AM
> To: AMBER Mailing List <amber.ambermd.org>
> Subject: Re: [AMBER] Apply Lennar-Jones potential between small molecules
>
> you might try using a distance restraint that has rk2=0, this will give no
> penalty for distances longer than r2 and a harmonic penalty below r2. You
> can define groups of atoms for COM distance restraints.
>
> check the manual for details (use the nmropt=1 option), and then create a
> restraint that looks something like this (making sure to edit the atom
> numbers, distances and force constants). igr1 and igr2 list the atoms in
> each COM group. r1/r2/r3/r4 define the distance points where the function
> changes. rk2 and rk3 are the force constants. The function is described in
> this tutorial:
> https://urldefense.com/v3/__http://ambermd.org/tutorials/advanced/tutorial4/__;!!NVzLfOphnbDXSw!TI_PpsbMCL8Whg8o7-3O7qAwmtKzGL2a_c4Q-vx_db-A5zB7SGvlObCAU4veBB_2eqzW$
>
> &wt
> type='END',
> &end
> &rst
> iat=-1,-1,
> igr1=1070,1130,
> igr2=1310,1325,1377,
> r1=1.0, r2=10.0, r3=900.0, r4=1000.0, rk2=10., rk3=0.0, &end &rst
> iat=0,
> &end
>
> On Wed, Feb 24, 2021 at 5:52 PM Ming Tang <m21.tang.qut.edu.au> wrote:
>
> > Dear list,
> >
> >
> > I have a system of protein with lot so small molecules solvated in a
> > water box. I want to apply force/potential between the centre of mass
> > a group of atoms in different small molecules to prevent them from
> > aggregation. I only know AMBER can define non-bounded interactions
> > between two atoms using LJEDIT in *.frcmod. Is there a way to define a
> > virtual particle as the centre of mass of a certain group of atoms?
> > Does anybody have any advice for me?
> >
> >
> >
> > Thanks,
> >
> > Ming
> >
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Received on Tue Mar 16 2021 - 06:00:02 PDT
