QuantumATK Forum

QuantumATK => General Questions and Answers => Topic started by: GJK on February 3, 2014, 08:17

Title: Non covalent interaction-reg
Post by: GJK on February 3, 2014, 08:17

Hi,

Suppose we form a device system (eg: ZGNR attached with anthracene) by attaching anthracene to ZGNR non covalently(meaning vander Waals interaction) ...Do we have to check for the interaction by rotating the  simulation box.Since it's a vander Waals interaction we do not have any bond being formed like covalent interaction.Kindly clarify!

Thanks in advance.

Title: Re: Non covalent interaction-reg
Post by: GJK on February 3, 2014, 18:21

Hi,

Waiting for your kind reply.

Title: Re: Non covalent interaction-reg
Post by: Anders Blom on February 3, 2014, 22:55

Rotating the simulation cell has no effect on the results.

Title: Re: Non covalent interaction-reg
Post by: GJK on February 5, 2014, 19:25

Then how to check whether the interaction is there is not.I mean by seeing it virtually on GUI.or if u can provide some tips kindly suggest me

Title: Re: Non covalent interaction-reg
Post by: Anders Blom on February 5, 2014, 21:14

Which interaction? I don't understand the question. If there are only vdW interactions between the molecule and the graphene then you need to run the simulation with vdW interactions, then you can optimize the structure in the usual way, like presented in http://quantumwise.com/documents/tutorials/latest/Grimme. You can of course manually the rotate or move the molecule on the surface and compute the binding energy as function of that.

Title: Re: Non covalent interaction-reg
Post by: GJK on February 8, 2014, 09:43

Then you mean to say that if we create an interaction manually between graphene and molecule we can confirm the interaction only by binding energy.

1.How to confirm Binding energy is correct or not?

2. My actual  question is if we create an interaction manually do we have to check whether interaction is there or not by rotating the simulation box ( by rotating the coordinates in GUI using the left side of the mouse).

3. Actually when i created such a system I found that it looks interacting.But on rotating the simulation box it appeared like no interaction.Kindly help me sir.

Title: Re: Non covalent interaction-reg
Post by: GJK on February 13, 2014, 09:06

Quote from: GJK on February  8, 2014, 09:43

Then you mean to say that if we create an interaction manually between graphene and molecule we can confirm the interaction only by binding energy.

1.How to confirm Binding energy is correct or not?

2. My actual  question is if we create an interaction manually do we have to check whether interaction is there or not by rotating the simulation box ( by rotating the coordinates in GUI using the left side of the mouse).

3. Actually when i created such a system I found that it looks interacting.But on rotating the simulation box it appeared like no interaction.Kindly help me sir.

Title: Re: Non covalent interaction-reg
Post by: Anders Blom on February 13, 2014, 09:37

1. Comparing to experiments I guess.
2. You don't create interactions manually in ATK. Interactions are introduced by the method use, DFT, van der Waals, etc.
3. You can't see if interactions are present or not. The bonds drawn in VNL are just there to guide the eye.