In my experience rk values near 30 work well for strong restraints. You can
work out the math to see how much deviation you get with thermal energy
about 1 kcal.
R2 and r3 can be set to the target value. R1 and r3 can be 30 degrees or
more away from that in either direction.
The details mostly matter if you initial structure doesn't match the target
value, or if you want to allow a range of motion. These don't seem to be
the case for you so try these suggestions.
On Wed, Feb 19, 2025, 1:58 AM Devid Sahu <ds890.snu.edu.in> wrote:
> Thanks for your suggestions. I have gone through the resources as per your
> recommendations and understood how to incorporate them into the simulation.
> However, I still have some confusion regarding the values of r1, r2, r3,
> r4, rk1, and rk2 for a dihedral restraint.
>
> I want to apply a dihedral restraint on the atoms with atom numbers 128,
> 127, 129, and 130 (O-C-N-H), which have a dihedral angle of -120.44°. I
> would like to maintain this dihedral angle throughout the simulation.
>
> Is there a specific method to determine the appropriate values for a given
> system, or are there any calculation techniques to help set these
> parameters?
>
> Thanks
>
> Devid
>
> On Wed, Feb 19, 2025 at 1:01 AM Carlos Simmerling <
> carlos.simmerling.gmail.com> wrote:
>
>> Hi Devid,
>> look at the Amber 24 manual, section 29. It describes the restraint
>> format. I suggest starting with rk values near 1 for distances, and maybe
>> 30 for angles and dihedrals (which have radian units in the force
>> constant).
>> you will need to set nmropt=1 to read the restraints (see section
>> 21.6.1).
>> You might also look at this link, scroll down to "please explain distance
>> restraints" https://ambermd.org/Questions/constraints.html
>>
>> On Tue, Feb 18, 2025 at 2:09 PM Devid Sahu <ds890.snu.edu.in> wrote:
>>
>>> Thank you for your response. I have simulated a system, but now I want
>>> to apply a dihedral restraint at 180 degrees. I understand that I need to
>>> specify the angle, force constant, and other parameters, but I am unsure
>>> how to determine their values and how to incorporate them into the
>>> prod.in file.
>>> *prod.in <http://prod.in/>: *
>>> Production
>>> &cntrl
>>> imin = 0, irest = 1, ntx = 5,
>>> ntb = 2, pres0 = 1.0, ntp = 1,
>>> taup = 2.0,
>>> cut = 8.0, ntr = 0,
>>> ntc = 2, ntf = 2,
>>> temp0 = 300.0,
>>> ntt = 3, gamma_ln = 1.0,
>>> nstlim = 400000000, dt = 0.002,
>>> ntpr = 100000, ntwx = 100000, ntwr = 10000,
>>> iwrap=1,
>>> ig=-1
>>> &rst
>>> iat=126,127,128,129,
>>> r1= ??, r2=??, r3=??, r4=??,
>>> rk2=??, rk3=??,
>>> &end
>>> /
>>> Any suggestions or guidance would be highly appreciated.
>>> Thanks
>>>
>>> On Tue, Feb 18, 2025 at 10:45 PM Carlos Simmerling <
>>> carlos.simmerling.gmail.com> wrote:
>>>
>>>> can you clarify what you need? Do you have a working simulation in
>>>> Amber, and just need to know the restraint format? or are you wanting to
>>>> learn how to do all of the simulation input?
>>>> section 29.1 of the Amber24 manual gives information on how to set up
>>>> the distance, angle and dihedral restraints.
>>>> also, have you looked at the tutorials at
>>>> https://ambermd.org/tutorials/? They can help you get started.
>>>>
>>>>
>>>>
>>>> On Tue, Feb 18, 2025 at 1:04 AM Devid Sahu via AMBER <amber.ambermd.org>
>>>> wrote:
>>>>
>>>>> Dear users
>>>>> I am looking to simulate an organic molecule with 208 atoms and need to
>>>>> apply restraints on two dihedral angles to a value 180 . I have
>>>>> explored
>>>>> some online resources but still lack clarity on how to specify the
>>>>> angles,
>>>>> atoms, and force constants. Could someone briefly guide me on the
>>>>> script
>>>>> and submission process? Forgive me as I am new in this field.
>>>>>
>>>>> Many thanks!!
>>>>> _______________________________________________
>>>>> AMBER mailing list
>>>>> AMBER.ambermd.org
>>>>> http://lists.ambermd.org/mailman/listinfo/amber
>>>>>
>>>>
_______________________________________________
AMBER mailing list
AMBER.ambermd.org
http://lists.ambermd.org/mailman/listinfo/amber
Received on Wed Feb 19 2025 - 04:30:02 PST
