VMD-L Mailing List

From: Axel Kohlmeyer (akohlmey_at_gmail.com)
Date: Fri Jun 12 2020 - 15:04:44 CDT

the problem lies in using .psf files. the .psf file format is meant to be
use with CHARMM, which bond, angle, dihedral and improper types are
implicitly defined by the atom types and pattern matching to the parameter
file. essentially, it is difficult to recover information that you have
deleted.

as far as i can tell, you have three options:
- you can use the "guess" functions in the topotools plugin to regenerate
bond, angle, dihedral types from atom types. ideally, you can then write
down the necessary xxx_coeff commands to fill in the parameters by
processing the data file with a text editor and comparing them to the
settings from the original data file.
- you prepare a water box without any solute and then use topotools and vmd
scripting to merge the two systems and delete overlaps
- same as before, but you use LAMMPS with using read_data twice.

neither will work fully automatically and has the risk of mixing things up
or that you may make a mistake that can go unnoticed (for a while).

HTH,
    axel.

On Fri, Jun 12, 2020 at 3:51 PM fan li <fanliqmul_at_gmail.com> wrote:

> Dear VMD users
>
> I have an input file for lammps in which Bond , angle , dihedral and
> improper type are properly defined. I have to add water to this structure,
> so I write the psf and pdb by "animate write" command. I have successfully
> added the water to psf and pdb file. However, the bond , angle , dihedral
> and improper type become unknown type. I checked and found it happened
> after animate write command. But the psf and pdb is necessary for adding
> water in vmd. I know the "topo guessangles" and similar command can be used
> to guess the angle type and others. However, the topology is very complex
> in my system so these commands do not generate the correct topology in
> comparison with the original input.So I wonder how to how to keep the bond
> , angle , dihedral and improper type after solvating the lammps data?
>
> Fan
>
>
>
> 

-- 
Dr. Axel Kohlmeyer  akohlmey_at_gmail.com  http://goo.gl/1wk0
College of Science & Technology, Temple University, Philadelphia PA, USA
International Centre for Theoretical Physics, Trieste. Italy.