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exercises:2014_uzh_molsim:chp_cu111

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exercise:mm_uzh:chp_cu111 [2014/06/30 14:05] – talirzexercise:2014_uzh_molsim:chp_cu111 [2014/10/15 13:42] – oschuett
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 The problem with this approach is that the lack of any surfaces makes it very hard for the liquid phase to nucleate in a small cell and within a reasonable simulation time. In such a simulation, melting will typically be observed only at temperatures significantly above $T_m$. The problem with this approach is that the lack of any surfaces makes it very hard for the liquid phase to nucleate in a small cell and within a reasonable simulation time. In such a simulation, melting will typically be observed only at temperatures significantly above $T_m$.
  
-{{ :exercise:mm_uzh:folded.png?700 |Half-molten Cu slab.}}+{{ folded.png?700 |Half-molten Cu slab.}}
  
 Here, we will use the so-called //phase coexistence technique// developed by [[doi>10.1007/978-94-011-1729-6|Ercolessi et al.]]. Here, we will use the so-called //phase coexistence technique// developed by [[doi>10.1007/978-94-011-1729-6|Ercolessi et al.]].
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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