VMD-L Mailing List

From: Udeshini Manatunga (mana.udeshini919_at_gmail.com)
Date: Fri May 08 2020 - 21:09:01 CDT

Hi Giacomo,

Thank you very much for your response. I used VDW and DynamicBonds
representations and reduced distance cutoff. Now It works.

Thank you.
Kind regards,
Udeshini

On Sat, May 9, 2020 at 12:43 AM Giacomo Fiorin <giacomo.fiorin_at_gmail.com>
wrote:

> 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
> 

-- 
Thanks.
Kind Regards,
Udeshini Manatunga
B.Sc. Eng.(Hons), AMIE(SL)
Mobile : (+61) 0408028804
email   : mana.udeshini919_at_gmail.com