self diffusion for UMCM-1 with 1-phenylamine
Closed this issue · 2 comments
Hi,
I have a problem to combine dihedral_style and improper_style for both MOF and guest molecule. I want to calculate the mean square displacement for 1-phenylamine in UMCM-1. However, the bond style, angle style, dihedral style, and improper style for MOF generated by lammps-interface is different with 1-phenylamine generated by LigParGen (OPLS-AA force field).
Input file for MOF:
units real
atom_style full
boundary p p p
pair_style lj/cut/coul/long 12.500
bond_style harmonic
angle_style hybrid fourier cosine/periodic
dihedral_style harmonic
improper_style fourier
kspace_style ewald 0.000001
special_bonds lj/coul 0.0 0.0 1.0
dielectric 1.0
pair_modify tail yes mix arithmetic
box tilt large
read_data data.UMCM1
Input file for 1-phenyamine by Ligpargen server:
units real
atom_style full
dimension 3
boundary p p p
pair_style lj/cut/coul/cut 20.0 20.0
pair_modify mix geometric
bond_style harmonic
angle_style harmonic
dihedral_style opls
improper_style cvff
special_bonds lj/coul 0.0 0.0 0.5
read_data 1phenylamine.lmp
They have different angle_style, dihedral_style, and improper_style. How can I combine my guest molecule and MOF to simulate the MSD with different angle, dihedral, and improper styles? In addition, can I change the improper style for MOF other than fourier because it require user-misc package but our HPC do not install it?
Thanks.
I think the issues you bring up are not related to the code we distribute, but with your understanding of LAMMPS. I would reference the lammps manual to answer how to combine dihedral styles. To solve your problem with the HPC I would suggest either contacting their IT people with your request, or installing LAMMPS in your local directory on the HPC. Failing that you can just install LAMMPS on your local computer and run the simulation.
I'm closing this but if I've misinterpreted your issue and it actually is related to lammps_interface, please re-open.
Can I combine MOF with guest molecule to generate one lammps input file by using lammps-interface?