sorry I meant use rk3=0, as in the example below.
On Thu, Feb 25, 2021 at 12:01 PM Carlos Simmerling <
carlos.simmerling.gmail.com> wrote:
> 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: http://ambermd.org/tutorials/advanced/tutorial4/
>
> &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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>>
>
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Received on Thu Feb 25 2021 - 09:30:03 PST
