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Re: [lammps-users] Amber FF
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Re: [lammps-users] Amber FF


From: Andrew Jewett <jewett@...1937...>
Date: Tue, 3 Oct 2017 17:04:41 -0700



On Tue, Oct 3, 2017 at 7:19 AM, Hossein Geraili <geraili.hsn@...1125.....> wrote:
E = K (theta - theta0)^2 + K_UB (r_13 - r_UB)^2
K_UB and r_UB(cross-term accounting for angle bending using 1,3 nonbonded interactions). How can I calculate these?

On Tue, Oct 3, 2017 at 5:33 PM, Axel Kohlmeyer <akohlmey@...24...> wrote:

On Tue, Oct 3, 2017 at 9:37 AM, Hossein Geraili <geraili.hsn@...24...> wrote:
Dear Lammps users,
I am using Amber force field optimized for my molecule, and it(in the article) has only two parameters for the angle. In the lammps section Howto for Amber angle_style charmm in introduced, but for charmm angle_style one should specify 4 parameters( 2Urey_Bradley parameters). I simulated with harmonic and I get a big error. Any idea where should I find these Urey_Bradley parameters? Actually the "distance between the 1,3 atoms in the harmonic potential" which is the Rub(one of the parameters, I can find. But, what about the force constant?

​here is the $5000 question: what is the force constant of term that does not exist?

axel.​


    For what it's worth, there are no Urey-Bradley parameters listed in the "gaff.dat" file distributed with AmberTools.  (I have not looked at the other AMBER force-field files.)  Don't know if this helps.  Where are you reading about these Urey-Bradley parameters?

-andrew

 
Best

--
Hosein Geraili Daronkola
M.Sc.Graduated of physical chemistry
Physical Chemistry,
Department of Chemistry,
Sharif University of Technology.
geraili_hosein@...7110...



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--
Dr. Axel Kohlmeyer  akohlmey@...24...  http://goo.gl/1wk0
College of Science & Technology, Temple University, Philadelphia PA, USA
International Centre for Theoretical Physics, Trieste. Italy.



--
Hosein Geraili Daronkola
M.Sc.Graduated of physical chemistry
Physical Chemistry,
Department of Chemistry,
Sharif University of Technology.
geraili_hosein@...7110...

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