VMD-L Mailing List

From: 刘志伟 (11924029_at_zju.edu.cn)
Date: Thu Sep 24 2020 - 06:00:44 CDT

Dear users,

My VMD version is 1.9.3.

I have a simulation with ReaxFF MD in LAMMPS. And I want to load trajectory file into VMD.

So I transfer data file into .psf in VMD and load .psf file and trajectory file. Here is the image. There is no bonds between atoms.

Here is data file. Because I use ReacFF MD to simulate lignin, data file's format has no angle and others information but atoms' coordinates. And the contol file in lammps is below. So how to load bonds information into VMD?

simulation_namelignin ! output files will carry this name + their specific ext

tabulate_long_range10000 ! denotes the granularity of long range tabulation, 0 means no tabulation
energy_update_freq 1

nbrhood_cutoff4.5 ! near neighbors cutoff for bond calculations in A
hbond_cutoff6.0 ! cutoff distance for hydrogen bond interactions
bond_graph_cutoff0.3 ! bond strength cutoff for bond graphs
thb_cutoff0.001 ! cutoff value for three body interactions

write_freq10000 ! write trajectory after so many steps
traj_titlelignin ! (no white spaces)
atom_info1 ! 0: no atom info, 1: print basic atom info in the trajectory file
atom_forces1 ! 0: basic atom format, 1: print force on each atom in the trajectory file
atom_velocities0 ! 0: basic atom format, 1: print the velocity of each atom in the trajectory file
bond_info1 ! 0: do not print bonds, 1: print bonds in the trajectory file
angle_info1 ! 0: do not print angles, 1: print angles in the trajectory file

Best,

David