Dear all,
Having studied LAMMPS documentation, I understood that if I need to create a system with bonds that are created and destroyed over time depending on atom locations, I should use Tersoff instead of fix bond/create command. I have 2 polymer chains, and would like region A of chain 1 to bond transiently with region B of polymer 2. I am using LJ units, atom_style angle. Could I ask whether this is the correct way to solve my problem?
Thank you very much!
with best wishes,
Anna
Dear all,
Having studied LAMMPS documentation, I understood that if I need to
create a system with bonds that are created and destroyed over time
depending on atom locations, I should use Tersoff instead of fix
bond/create command. I have 2 polymer chains, and would like region A of
chain 1 to bond transiently with region B of polymer 2. I am using LJ
units, atom_style angle. Could I ask whether this is the correct way to
solve my problem?
this is not as easy. there usually is not only _the_ one correct way,
but different levels of approximation. question is, what is the nature
of the bonding between the two regions and how to "decide" when
a bond (and/or how many?) are formed. using a bond order potential
is one way to do this, but you'll have to parameterize it, unless you
have atoms that represent elements/systems that are already
parameterized (unlikely from what you write).
can you put into some kind of mathematical formula how to
compute what atom should bond to which one at what strength?
axel.
Dear all,
Having studied LAMMPS documentation, I understood that if I need to
create a system with bonds that are created and destroyed over time
depending on atom locations, I should use Tersoff instead of fix
bond/create command. I have 2 polymer chains, and would like region A of
chain 1 to bond transiently with region B of polymer 2. I am using LJ
units, atom_style angle. Could I ask whether this is the correct way to
solve my problem?
this is not as easy. there usually is not only _the_ one correct way,
but different levels of approximation. question is, what is the nature
of the bonding between the two regions and how to "decide" when
a bond (and/or how many?) are formed. using a bond order potential
is one way to do this, but you'll have to parameterize it, unless you
have atoms that represent elements/systems that are already
parameterized (unlikely from what you write).
can you put into some kind of mathematical formula how to
compute what atom should bond to which one at what strength?
axel.
Tersoff is not typically a potential for polymeric systems.
You might look at fix bond/create and fix bond/break.
Steve