QuantumATK Forum

QuantumATK => General Questions and Answers => Topic started by: jeong9090 on February 20, 2018, 20:12

Title: Define Nitrogen gas molecule bonding
Post by: jeong9090 on February 20, 2018, 20:12

Hi,

I want to put N2 gas molecules between graphene and Cu substrate.

I have tried to use molecule builder on VNL.

When I make two mono-nitrogen atoms as attached pictures, I tried to define the bonding between two nitrogen atom because nitrogen gas is N2 but I could not.

I will run MD simulation with this geometry. For running MD, I will use LAMMPS and define interatomic potential for each material and N2 gas.

In this case, do I need to make the bond of nitrogen atoms for N2 or I can put mono-nitrogen atom into the interface?

I'd appreciate if you let me know that.

Thanks,

Jaeyoung Jeong

 

Title: Re: Define Nitrogen gas molecule bonding
Post by: Petr Khomyakov on February 21, 2018, 09:41

You can change the N atom separation distance by using the Move Tool in the Builder, https://docs.quantumwise.com/tutorials/builder_manual/builder_movetool/builder_movetool.html. You may set the distance to experimental value that must be available in the literature, or do a separate geometry optimization calculation for the N2 molecule to find the equilibrium distance.

Title: Re: Define Nitrogen gas molecule bonding
Post by: jeong9090 on February 21, 2018, 19:58

Hi,

Thank you for a reply.

Can you let me know where I can set the distance?

I can find the distance value but I don't know where I can set it at VNL.

Thanks,

Jaeyoung

Title: Re: Define Nitrogen gas molecule bonding
Post by: Petr Khomyakov on February 22, 2018, 10:50

There is a measure tool for measuring distances between atoms in the Builder, so that  you may use it in combination with the Move Tool. Another option is to use the Coordinate List in the Coordinate Tools where you could manually set the coordinates of the two N atoms such that the distance between the atoms is equal to the equilibrium distance or any distance of your choice.

Title: Re: Define Nitrogen gas molecule bonding
Post by: jeong9090 on February 22, 2018, 17:38

Thank you so much