Bond atom missing - Rerun

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1

Hello,

I’m am trying to learn how to use the rerun command. I have an XYZ data file (generated from VMD of a previous simulation) with the coordinated wrapped into the PBC box. When I run the input script below, I get “bond missing” error. Any ideas for what I’m doing wrong?

Thanks for the help,
Stacey

“”""

I suppose we should try to run a simulation?

units real
atom_style full
boundary p p f

read_data Slab_1.data

pair_style lj/cut/coul/cut 10.0 12.0
bond_style harmonic
angle_style harmonic
dihedral_style fourier

special_bonds amber

2

Hello,

I’m am trying to learn how to use the rerun command. I have an XYZ data file (generated from VMD of a previous simulation) with the coordinated wrapped into the PBC box. When I run the input script below, I get “bond missing” error. Any ideas for what I’m doing wrong?

you must not wrap bonds.
you should not use .xyz files for periodic systems, as the .xyz file does not contain simulation box information.

axel.

3

Thanks Axel

I wrote out a lammpstrj file with VMD on the unwrapped coordinates and changed the rerun command to:

“”"
rerun input.lammpstrj dump x y z box no wrapped no

“”"

Thank did the trick.

Thanks again,
Stacey