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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: Mon, 23 Oct 2017 16:27:19 +0800

Thank you very much for your reply.

The "spherical" dihedral style is usefull.


Best,
Zhuangli Cai
 
From: Andrew Jewett
Date: 2017-10-16 08:32
To: Zhuangli cai
CC: lammps; Steve Plimpton
Subject: Re: [lammps-users] Bonded atoms far aprt in Coarse-grained simulation


On Oct 12, 2017 10:20 AM, "Zhuangli cai" <980046700@...1204...> wrote:
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.

Yes.  There is a singularity in the dihedral forces whenever the bond angle between any 3 of them approaches 180 degrees.  So you cannot use traditional dihedral forces in this case (even if you use a small timestep).  The "spherical" dihedral style was designed to solve this problem.  For details see:

http://lammps.sandia.gov/doc/dihedral_spherical.html

Note: If the equilibrium rest angle is close to 180 degrees, you may need to use a more complicated expansion than the simple 3-term example shown on that web page, but any periodic function of phi, theta1, and theta2 can be approximated using this dihedral style, and you do not need to define separate angle interactions between atoms 1,2,3 and 2,3,4.  (However you must insure that the bond distances always remain reasonably large, preferably > 1 Angstroms.)

Cheers
Andrew

P.S. You will have to make sure you compiled LAMMPS with the USER-MISC package installed.  For details about that, see:
http://lammps.sandia.gov/doc/Section_start.html#start-3




Best,
Zhuangli Cai
 
Date: 2017-10-12 21:00
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?

Steve

On Sun, Oct 1, 2017 at 1:12 AM, Zhuangli cai <980046700@...1497...04...> 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.


Best,
Zhuangli Cai

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