Hi all,
In my system I have 2 particles connected by harmonic bond. And for
this interaction I have specified a bond coefficient.
Now, I wish to apply a LJ interaction, via lj/cut command,
on top of harmonic interaction. Will it work then ?
I am doing this. Somehow it is not working.
In a short, there dynamics is governed by the harmonic interaction only.
LJ interaction is not taking count.
Can you please give me any idea to over come it.
Best,
You will have to be a bit more specific than “it is not working”. What do you observe and what did you expect to observe? What input script(s)/data files are you using?
I can only answer your first question: Yes, it should definitely work, as these systems work fine for me. The problem must be in your input script or data file.
You will have to be a bit more specific than "it is not working". What do
you observe and what did you expect to observe? What input script(s)/data
files are you using?
Yes, I should mention it elaborately .
I have attached bot the script and the data file.
As the data file reads, initially the atoms are apart by 2 unit length
distance and their equilibrium length is 1 unit.
Where as in the 'pair_style lj/cut' I have set 'sigma' as 1.5 unit
length.
So, my expectation is that they should settle down when they are separated
by 1.5 unit length distance.
But, what happens, it is settling down at 1 unit length separation.
This is what I cant understand.
I can only answer your first question: Yes, it should definitely work, as
these systems work fine for me. The problem must be in your input script
or
data file.Hi all,
In my system I have 2 particles connected by harmonic bond. And for
this interaction I have specified a bond coefficient.
Now, I wish to apply a LJ interaction, via lj/cut command,
on top of harmonic interaction. Will it work then ?I am doing this. Somehow it is not working.
In a short, there dynamics is governed by the harmonic interaction
only.
LJ interaction is not taking count.
Can you please give me any idea to over come it.Best,
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Best,
in.test (1.94 KB)
data.lammps (449 Bytes)
Hi all,
In my system I have 2 particles connected by harmonic bond. And for
this interaction I have specified a bond coefficient.
Now, I wish to apply a LJ interaction, via lj/cut command,
on top of harmonic interaction. Will it work then ?
this is a *very* unusual model. typically, when you have explicit
bonded interactions, non-bonded interactions between the atoms that
are bonded are ignored. this is called 1-2 exclusions and only
computed between periodic images (if they are within the cutoff). same
goes for 1-3 and 1-4 neighbors for angles and dihedrals. the scaling
factors for this are controlled with the special_bonds command.
please update your basic force field knowledge by re-reading the
corresponding chapters in your favorite text book on MD and their
force fields before continuing.
axel.
Also, it seems you need to read the documentation more properly and think about how to map the system you want to simulate into a proper setup for LAMMPS. For example, the second parameter for pair_coeff in the case of Lennard-Jones is not the equilibrium spacing but the distance at which the potential is 0.
Also, it is a bad idea to use two thermostats at the same time, which you seem to do in your input script.
The special_bonds command Axel indicated allows you
to turn on/off/scale LJ (or pair) interactions between atoms
bonded to each other. For 2 atoms connected by a harmonic
bond, you can have bond + alpha*LJ, where alpha is any scale
factor from 0.0 to 1.0. The default is 0.0.
Steve
The special_bonds command Axel indicated allows you
to turn on/off/scale LJ (or pair) interactions between atoms
bonded to each other. For 2 atoms connected by a harmonic
bond, you can have bond + alpha*LJ, where alpha is any scale
factor from 0.0 to 1.0. The default is 0.0.Steve
Thank you very much Steve and Axel.
Now its working as per I wished to.
Thanks once again.