Dear SIESTA users,
I am using SIESTA (4.1-b3) code for the relaxation of graphene-metal oxide interface structure. It has been seen that after few 'vc-relaxation' steps, some atoms of the structure come outside the unit cell. Now, as I am continuing with the further simulation steps, (it seems to me ) these outside atoms may not get proper boundary/periodic conditions and these boundary atoms may get wrongly interacted with other neighbor atoms, which results in a distorted structure at end of the optimization.
Now I am bit confused as I don't know whether the final relaxed structure is correct or not.
I am very new to the SIESTA code. Could you please help me to clear my doubt?
I am looking forward to hearing from you.
Thanking you.
With regards,
Bibhas
The distorted in structure is many times because of the incorrect inputs that do not assign the accurate bond lengths and angles, For more detail see,
https://www.researchgate.net/post/Why_bonds_breaks_after_the_optimization_in_Gaussian09
https://www.researchgate.net/post/Optimizing_ligands_before_running_molecular_docking_simulation
The distorted in structure is many times because of the incorrect inputs that do not assign the accurate bond lengths and angles, For more detail see,
https://www.researchgate.net/post/Why_bonds_breaks_after_the_optimization_in_Gaussian09
https://www.researchgate.net/post/Optimizing_ligands_before_running_molecular_docking_simulation
The distorted in structure is many times because of the incorrect inputs that do not assign the accurate bond lengths and angles, For more detail see,
https://www.researchgate.net/post/Why_bonds_breaks_after_the_optimization_in_Gaussian09
https://www.researchgate.net/post/Optimizing_ligands_before_running_molecular_docking_simulation
Dear Jappor,
Thank you very much for your kind reply. However, I have few more doubts...
I have seen that as long as atoms are inside the unit cell, no problem comes. But as atoms start coming outside the cell the structure starts distorting.
Is this coming due to the use of wrong basis set in SIESTA????
My structure is the stack of Graphene Oxide slab and a SnO2 slab on the top..
One has hexagonal crystal structure and other has tetragonal. Does it come due to excess stress generated within the system????
I am looking forward for your kind answer.
Thanking you.
Bibhas
- Badges
- Science topic
- Similar topics
- Physical Sciences
- Atomic, Molecular and Optical Physics
- Atoms