Dear all,
I’m running MD simulation by LAMMPS coupling with Materials Studio. I used Materials Studio to build the structure, and imported it into Lammps, and used Clayff to run the simulation. Since clayff only calculates bonds for water molecules and hydroxyls, so when I imported the structure, I only kept those bonds. With clayff, intermolecular interactions were calculated as the sum of an electrostatic term for all Coulomb interactions between partial atomic charges, a 12-6 Lennard-Jones term for the short-range van der Waals dispersive interactions, and the bond stretch and angle bend terms of hydroxyl groups. So I used the following potentials:
bonded interactions: bond stretching and angle bending in harmonic form
bond_style harmonic
angle_style harmonic
neighbor list skin distance 3?
neighbor 3.0 bin
neighbor list build:
neigh_modify every 2 delay 0 check yes one 3000
nonbonded interactions: Lennard-Jones with 12.5?cut-off and long range Coulomb
pair_style lj/cut/coul/long 12.5
pair_modify mix arithmetic
ewald summation method for long range Coulomb
kspace_style ewald 1.0e-4
However, when I imported the trajectory back to Materials Studio, I found out that lots of bonds in water molecules were gone. Why would this happened, did I use the wrong potential or something wrong when I use the tools to import/export the structure?
I appreciate your help.
Regards,
Jingjing Bu
Dear all,
I’m running MD simulation by LAMMPS coupling with Materials Studio. I used Materials Studio to build the structure, and imported it into Lammps, and used Clayff to run the simulation. Since clayff only calculates bonds for water molecules and hydroxyls, so when I imported the structure, I only kept those bonds. With clayff, intermolecular interactions were calculated as the sum of an electrostatic term for all Coulomb interactions between partial atomic charges, a 12-6 Lennard-Jones term for the short-range van der Waals dispersive interactions, and the bond stretch and angle bend terms of hydroxyl groups. So I used the following potentials:
bonded interactions: bond stretching and angle bending in harmonic form
bond_style harmonic
angle_style harmonic
neighbor list skin distance 3?
neighbor 3.0 bin
neighbor list build:
neigh_modify every 2 delay 0 check yes one 3000
nonbonded interactions: Lennard-Jones with 12.5?cut-off and long range Coulomb
pair_style lj/cut/coul/long 12.5
pair_modify mix arithmetic
ewald summation method for long range Coulomb
kspace_style ewald 1.0e-4
However, when I imported the trajectory back to Materials Studio, I found out that lots of bonds in water molecules were gone. Why would this happened, did I use the wrong potential or something wrong when I use the tools to import/export the structure?
This really is a question about materials studio and not lammps.
Axel