VMD-L Mailing List

From: Giacomo Fiorin (giacomo.fiorin_at_gmail.com)
Date: Fri May 08 2020 - 09:42:56 CDT

Hi Udeshini, a first approximation in VMD for displaying bonds that form or
break during a simulation is using a VDW representation with scaled-down
radii to show the atoms as spheres, *plus* an additional DynamicBonds
representation to draw cylinders along bonds that are formed. With a
little adjustment, this is just like the CPK representation.

Note that this will place bonds using a simple distance cutoff and not the
reaxff scoring function.

Giacomo

On Fri, May 8, 2020 at 5:27 AM Udeshini Manatunga <
mana.udeshini919_at_gmail.com> wrote:

> Hi VMD users,
>
> I'm a beginner to VMD and Lammps. I'm trying to simulate hydration
> reaction between CaO and water using reaxff with lammps. I hope the water
> will break into OH- and H+ during the simulation. I didn't define any bonds
> of the water molecules as reaxff doesn't need bond details. I dump the
> lammps trajectory file(.lammpstrj) and visualize it as follows,
> 1) When I visualize the trajectory file with psf file, I couldn't see any
> bonds (I think this is because there are no bonds in the data file)
> 2) When I directly input the trajectory file, there is an extra bond
> between H atoms in the water molecule.
>
> So, How do I correctly visualize my system? Any reply would be
> greatly appreciated. I attached the data file and the input file.
>
>
> 

-- 
Giacomo Fiorin
Associate Professor of Research, Temple University, Philadelphia, PA
Research collaborator, National Institutes of Health, Bethesda, MD
http://goo.gl/Q3TBQU
https://github.com/giacomofiorin