Dear All users
I like simulating pure butane,
I can not understand the meaning of this sentence and If I want to start my simulation, How can
I specify parameters for pairs and angles :
A part of paper:
The skeleton of a butane molecule is made of four points coinciding with the positions of the C nuclei: all C-C bonds are rigid with an identical length of 1.53 A(? parameters is removed), the angles between adjacent bonds are constant and equal to 109.28(?)
Dear All users
I like simulating pure butane,
I can not understand the meaning of this sentence and If I want to start my
simulation, How canI specify parameters for pairs and angles :
A part of paper:
The skeleton of a butane molecule is made of four points coinciding with the
positions of the C nuclei: all C-C bonds are rigid with an identical length
of 1.53 A(? parameters is removed), the angles between adjacent bonds are
constant and equal to 109.28(?)
if you keep a bond or an angle rigid, you don't need a force constant,
only the equilibrium distance or angle.
in lammps you do provide the bond/angle and can specify the force
constant to any value you like.
mind you, the model you describe, cannot be exactly implemented in LAMMPS.
fix shake doesn't support this kind of model.
axel.
Dear All users
I like simulating pure butane,
cool
I can not understand the meaning of this sentence and If I want to start my
simulation, How can I specify parameters for pairs and angles :A part of paper:
The skeleton of a butane molecule is made of four points coinciding with the
positions of the C nuclei: all C-C bonds are rigid with an identical length
of 1.53 A(? parameters is removed), the angles between adjacent bonds are
constant and equal to 109.28(?)
I attached a picture of what I think this means. (I could be wrong.)
If you want to include hydrogen atoms, you will still need the CH
distance(s), CCH, HCH angles and HCCH and HCCC dihedrals (and CHHH and
CCHH impropers).
I hope this gets you started.
Andrew
Ali,
Here some dessert after Andrew's main course 
You can find Trappe-UA parameters at the link below. If you search by
molecular name, butane is one of the compounds included in the
database.
http://www.chem.umn.edu/groups/siepmann/trappe/intro.php
Trappe-UA employs fixed bonds. You could define harmonic bonds between
the atoms to be used within Lammps. The bond stiffness can be taken
from the Amber or OPLS force fields. Adding harmonic bonds has been
shown to improve the Trappe-UA predictions when it comes to
calculating physical properties like liquid viscosities. Beware of the
energy units used in the database.
Carlos
Dear Calos,
Thank you for your reply,
Yes, I have performed two simulation with two ff, OPLS-UA and Trapp,