Re: [AMBER] Apply Lennar-Jones potential between small molecules

From: Carlos Simmerling <carlos.simmerling.gmail.com>
Date: Tue, 16 Mar 2021 08:32:12 -0400

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
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