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exercises:2014_uzh_molsim:chp_cu111

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exercise:mm_uzh:chp_cu111 [2014/06/30 11:22] – talirzexercise:mm_uzh:chp_cu111 [2014/07/03 17:34] – talirz
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   - Visualize an optimized slab with vmd, draw the simulation box and create a replica along x,y and z to familiarize yourself with the geometry. Why is the //slab geometry// used in atomistic simulations? What are the relevant convergence parameters? (2P)   - Visualize an optimized slab with vmd, draw the simulation box and create a replica along x,y and z to familiarize yourself with the geometry. Why is the //slab geometry// used in atomistic simulations? What are the relevant convergence parameters? (2P)
-  - The initial geometries were cut from a perfect bulk Cu crystal. Why do they still need to be optimized? Do //all// of them need to be optimized?+  - The initial geometries were cut from a perfect bulk Cu crystal. Why do they still need to be optimized? 
 +  - **BONUS** Do //all// of them need to be optimized?
   - How many layers are required to achieve a bulk environment in the center of the slab? //Hint:// Study the energy $\triangle E(N)$ as a function of $N$. You may want to use the script ''analyze-slabs.sh''.   - How many layers are required to achieve a bulk environment in the center of the slab? //Hint:// Study the energy $\triangle E(N)$ as a function of $N$. You may want to use the script ''analyze-slabs.sh''.
   - Calculate the surface energy $\sigma$ of Cu(111).   - Calculate the surface energy $\sigma$ of Cu(111).
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   - Read through section 2.1 of the work by [[doi>10.1140/epjb/e2010-00038-1|Pignedoli et al.]] and report the methods used for the different kinds of interactions. //Note:// In ''geo.in'', we are using a less computationally demanding method to treat the QM part. (2P)   - Read through section 2.1 of the work by [[doi>10.1140/epjb/e2010-00038-1|Pignedoli et al.]] and report the methods used for the different kinds of interactions. //Note:// In ''geo.in'', we are using a less computationally demanding method to treat the QM part. (2P)
   - Look inside ''geo.in'' and describe its overall structure. How is the coupling of QM and MM represented in the input file?   - Look inside ''geo.in'' and describe its overall structure. How is the coupling of QM and MM represented in the input file?
-  - Visualize the optimized geometry with VMD and render a nice image for the report.+  - Run the geometry optimization, visualize the optimized geometry with VMD and render a nice image for the report.
   - What is the adsorption height of the molecule?   - What is the adsorption height of the molecule?
   - In order to calculate the //binding energy// of CHP adsorbed on Cu(111), perform geometry optimizations of the isolated molecule as well as the clean slab. //Hint:// Start from ''geo.in'' and remove the sections that you don't need. Make sure that the ''.xyz'' files you use in the input only contain the atoms you need for the respective calculation.   - In order to calculate the //binding energy// of CHP adsorbed on Cu(111), perform geometry optimizations of the isolated molecule as well as the clean slab. //Hint:// Start from ''geo.in'' and remove the sections that you don't need. Make sure that the ''.xyz'' files you use in the input only contain the atoms you need for the respective calculation.
exercises/2014_uzh_molsim/chp_cu111.txt · Last modified: 2020/08/21 10:15 by 127.0.0.1