VMD-L Mailing List

From: Josh Vermaas (joshua.vermaas_at_gmail.com)
Date: Thu Sep 24 2020 - 09:57:06 CDT

Hi David,

For reactive force fields, I frequently see folks using "dynamic bonds"
representations, since the bond information won't be static like VMD
expects. If you wanted to show the bonds at time 0, not loading a psf and
using VMD's distance-based heuristics might be a pretty good idea.

-Josh

On Thu, Sep 24, 2020 at 5:26 AM 刘志伟 <11924029_at_zju.edu.cn> wrote:

> 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_name lignin ! output files will carry this name + their
> specific ext
>
> tabulate_long_range 10000 ! denotes the granularity of long range
> tabulation, 0 means no tabulation
> energy_update_freq 1
>
> nbrhood_cutoff 4.5 ! near neighbors cutoff for bond calculations in A
> hbond_cutoff 6.0 ! cutoff distance for hydrogen bond interactions
> bond_graph_cutoff 0.3 ! bond strength cutoff for bond graphs
> thb_cutoff 0.001 ! cutoff value for three body interactions
>
> write_freq 10000 ! write trajectory after so many steps
> traj_title lignin ! (no white spaces)
> atom_info 1 ! 0: no atom info, 1: print basic atom info in the
> trajectory file
> atom_forces 1 ! 0: basic atom format, 1: print force on each atom in
> the trajectory file
> atom_velocities 0 ! 0: basic atom format, 1: print the velocity of
> each atom in the trajectory file
> bond_info 1 ! 0: do not print bonds, 1: print bonds in the trajectory
> file
> angle_info 1 ! 0: do not print angles, 1: print angles in the
> trajectory file
>
> Best,
>
> David
>
>
>