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Re: [lammps-users] Bonded atoms far aprt in Coarse-grained simulation
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Re: [lammps-users] Bonded atoms far aprt in Coarse-grained simulation

From: "Zhuangli cai" <980046700@...1204...>
Date: Thu, 12 Oct 2017 22:06:06 +0800

Thank you for your attention.

I came up with the dihedral potential parameters myself for fitting the dihedral angle distribution of  supperatoms from coarse-grained simulation to one from all-atom simulation. But the coarse-grained simulations with dihedral potential always fail.

I observed the configuration(the picture is attached) of the coarse-grained chain when the bonded atoms would be far apart at the next timestep and found that the angle of three neighborest atoms is 179.9954 degree(near to 180 degree). I think it may be this angle(near to 180 degree) resulting in the bad dynamics. When the angle is very close to 180 degree, the distance between atom 0 and bond formed by atom 1 and atom 2 is so short(only 0.000377 Angstrom) that the force from the torque resulted from dihedral potential to atome 0 becomes very large. And then the atom 0 will fly away. So is it right that the dihedral potential can not be used when the angles are able to be close to 180 degree? Above it is my explaination. However, the fact is that the atom 1 flew away. It is so werid. I do not understand the fundamental algorithms about lammps well, so it is just my thought from the physcial reasoning.

Zhuangli Cai
From: Steve Plimpton
Date: 2017-10-12 21:00
To: Zhuangli cai
CC: lammps-users
Subject: Re: [lammps-users] Bonded atoms far aprt in Coarse-grained simulation
So if you are adding a dihedral term to the force field and it is causing bad
dynamics, then the dihedral term must be causing it.  Where
did you get the dihedral term and its parameters?  Is it from
the literature?  Have others run good dynamics with it?
Or did you come up with it yourself?


On Sun, Oct 1, 2017 at 1:12 AM, Zhuangli cai <980046700@...1204...> wrote:
Dear lammps user,

I am doing a coarse-grained simulation about a single polymer chain using LAMMPS (1 Mar 2016-ICMS). Firstly, I ran a NVT simulation with LJ potential as pair potential, Morse potential as bond potential and  cosine/squared potential as angle potential and then it is all right. However, when I added a dihedral potential to the coarse-grained model, the bonded atoms of the polymer chain are far apart from each other and  blowing away from the box. I also try the latest version of LAMMPS to run the simulation but the blowing still occurs.

The input script, data file and log file all are attached.  The log file only includes the 2000 timesteps in which some atoms were blow away from the box. 

It is werid that the bonded atoms are far apart from each other because the bonded interaction is strong enough. I also plot the curve of  Kinetic energy and potential energy of the system when the boned atoms are far apart and they are showed below.
In the above two picture, it is strange that the kinetic energy increases suddenly prior to the potential energy. It is usual that the large force from the steep potential gradient  results in the incresing of velocity and then kinetic energy. Is it possible that the calculation of velocity of a certain atom when simulating is incorrect? Or can anyone explains this sitiuation? 

Any advice is welcome. Thanks for your attention and efforts in advance.

Zhuangli Cai

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