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events:2016_summer_school:qmmm [2016/08/25 20:58] mwatkinsevents:2016_summer_school:qmmm [2020/08/21 10:15] (current) – external edit 127.0.0.1
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 School of Mathematics and Physics, University of Lincoln, UK School of Mathematics and Physics, University of Lincoln, UK
  
-http://www.cp2k.org+https://www.cp2k.org
  
 {{https://www.cp2k.org/lib/tpl/cp2kwiki/images/logo.png }} {{https://www.cp2k.org/lib/tpl/cp2kwiki/images/logo.png }}
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 $$ $$
  
-Periodic electric field uses the Berry phase formalism of the [[http://journals.aps.org/prb/abstract/10.1103/PhysRevB.47.1651|Modern Theory of Polarizablility]] and can be used for periodic systems.+Periodic electric field uses the Berry phase formalism of the [[https://journals.aps.org/prb/abstract/10.1103/PhysRevB.47.1651|Modern Theory of Polarizablility]] and can be used for periodic systems.
  
-{{http://pubs.acs.org/appl/literatum/publisher/achs/journals/content/jpclcd/2016/jpclcd.2016.7.issue-14/acs.jpclett.6b01127/20160725/images/medium/jz-2016-01127a_0005.gif}}+{{https://pubs.acs.org/appl/literatum/publisher/achs/journals/content/jpclcd/2016/jpclcd.2016.7.issue-14/acs.jpclett.6b01127/20160725/images/medium/jz-2016-01127a_0005.gif}}
  
-[[http://pubs.acs.org/doi/abs/10.1021/acs.jpclett.6b01127|Computing the Kirkwood g-Factor by Combining Constant Maxwell Electric Field and Electric Displacement Simulations: Application to the Dielectric Constant of Liquid Water, Chao Zhang, Jürg Hutter, and Michiel Sprik, J. Phys. Chem. Lett., 2016, 7 (14), pp 2696–2701]]+[[https://pubs.acs.org/doi/abs/10.1021/acs.jpclett.6b01127|Computing the Kirkwood g-Factor by Combining Constant Maxwell Electric Field and Electric Displacement Simulations: Application to the Dielectric Constant of Liquid Water, Chao Zhang, Jürg Hutter, and Michiel Sprik, J. Phys. Chem. Lett., 2016, 7 (14), pp 2696–2701]]
  
 ==== QM/MM ==== ==== QM/MM ====
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 Well known method is QMMM, one main strand arose from the bio community - aiming to accurately model active sites in proteins Well known method is QMMM, one main strand arose from the bio community - aiming to accurately model active sites in proteins
  
-{{ exercises:2016_summer_school:rhodopsin.png?320}}+{{exercises:2016_summer_school:rhodopsin.png?320}}
  
 typically the active site was surrounded by a finite number of classical point charges typically the active site was surrounded by a finite number of classical point charges
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 An attractive feature of CP2K's QMMM implementation is that it can be fully periodic, or anything from a cluster to a 3D system. An attractive feature of CP2K's QMMM implementation is that it can be fully periodic, or anything from a cluster to a 3D system.
  
-{{exercises:2016_summer_school:qmmm_island.png?320 | 3D system}}  +{{exercises:2016_summer_school:qmmm_island.png?320 | 3D system }} 
 {{ exercises:2016_summer_school:qmmm_sandwich.png?320|2D sandwich system}}  {{ exercises:2016_summer_school:qmmm_sandwich.png?320|2D sandwich system}} 
  
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 the final term $R_{low} (|\mathbf{r}-\mathbf{R}_a|)$ is the residual part of the function not represented by the Gaussians, and should be rather smooth. the final term $R_{low} (|\mathbf{r}-\mathbf{R}_a|)$ is the residual part of the function not represented by the Gaussians, and should be rather smooth.
  
-{{http://pubs.acs.org/appl/literatum/publisher/achs/journals/content/jctcce/2005/jctcce.2005.1.issue-6/ct050123f/production/images/medium/ct050123ff00001.gif}}+The number of terms in the sum $N_g$ is set by the input variable ''USE_GEEP_LIB'' 
 + 
 +{{https://pubs.acs.org/appl/literatum/publisher/achs/journals/content/jctcce/2005/jctcce.2005.1.issue-6/ct050123f/production/images/medium/ct050123ff00001.gif}}
  
-[[http://pubs.acs.org/doi/full/10.1021/ct050123f|An Efficient Real Space Multigrid QM/MM Electrostatic Coupling, Teodoro Laino, Fawzi Mohamed , Alessandro Laio , and Michele Parrinello, J. Chem. Theory Comput., 2005, 1 (6), pp 1176–1184]]+[[https://pubs.acs.org/doi/full/10.1021/ct050123f|An Efficient Real Space Multigrid QM/MM Electrostatic Coupling, Teodoro Laino, Fawzi Mohamed , Alessandro Laio , and Michele Parrinello, J. Chem. Theory Comput., 2005, 1 (6), pp 1176–1184]]
  
 == Short range electrostatic coupling - collocating the potential == == Short range electrostatic coupling - collocating the potential ==
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 </code> </code>
  
-{{http://pubs.acs.org/appl/literatum/publisher/achs/journals/content/jctcce/2005/jctcce.2005.1.issue-6/ct050123f/production/images/medium/ct050123ff00002.gif}}+{{https://pubs.acs.org/appl/literatum/publisher/achs/journals/content/jctcce/2005/jctcce.2005.1.issue-6/ct050123f/production/images/medium/ct050123ff00002.gif}}
  
 The short range part is put onto grids in much the same manner as in the GPW method. The short range part is put onto grids in much the same manner as in the GPW method.
  
-[[http://pubs.acs.org/doi/full/10.1021/ct050123f|An Efficient Real Space Multigrid QM/MM Electrostatic Coupling, Teodoro Laino, Fawzi Mohamed , Alessandro Laio , and Michele Parrinello, J. Chem. Theory Comput., 2005, 1 (6), pp 1176–1184]]+[[https://pubs.acs.org/doi/full/10.1021/ct050123f|An Efficient Real Space Multigrid QM/MM Electrostatic Coupling, Teodoro Laino, Fawzi Mohamed , Alessandro Laio , and Michele Parrinello, J. Chem. Theory Comput., 2005, 1 (6), pp 1176–1184]]
  
 == Periodic embedding == == Periodic embedding ==
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 section. The default is non periodic embedding. section. The default is non periodic embedding.
  
-{{http://pubs.acs.org/appl/literatum/publisher/achs/journals/content/jctcce/2006/jctcce.2006.2.issue-5/ct6001169/production/images/medium/ct6001169f00001.gif}}+{{https://pubs.acs.org/appl/literatum/publisher/achs/journals/content/jctcce/2006/jctcce.2006.2.issue-5/ct6001169/production/images/medium/ct6001169f00001.gif}}
  
-[[http://pubs.acs.org/doi/abs/10.1021/ct6001169|An Efficient Linear-Scaling Electrostatic Coupling for Treating Periodic Boundary Conditions in QM/MM Simulations, Teodoro Laino, Fawzi Mohamed, A. Laio, M. Parrinello, JCTC, 2, 1370 (2006)]]+[[https://pubs.acs.org/doi/abs/10.1021/ct6001169|An Efficient Linear-Scaling Electrostatic Coupling for Treating Periodic Boundary Conditions in QM/MM Simulations, Teodoro Laino, Fawzi Mohamed, A. Laio, M. Parrinello, JCTC, 2, 1370 (2006)]]
  
 == Long range coupling == == Long range coupling ==
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 see this [[https://www.cp2k.org/exercises:2015_cecam_tutorial:urea|exercise]] see this [[https://www.cp2k.org/exercises:2015_cecam_tutorial:urea|exercise]]
  
-## Input files+===== Input files =====
  
-Example setup for KCl that we used [here](http://onlinelibrary.wiley.com/doi/10.1002/jcc.23904/full).+Example setup for KCl that we used [[https://onlinelibrary.wiley.com/doi/10.1002/jcc.23904/full| here]].
  
-{{http://onlinelibrary.wiley.com/store/10.1002/jcc.23954/asset/image_n/jcc23954-toc-0001.png?v=1&s=6f79087c34654bcc15eda422e9c03888b4ee9550}}+{{https://onlinelibrary.wiley.com/store/10.1002/jcc.23954/asset/image_n/jcc23954-toc-0001.png?v=1&s=6f79087c34654bcc15eda422e9c03888b4ee9550}}
  
 We need to define the whole system as normal We need to define the whole system as normal
events/2016_summer_school/qmmm.1472158690.txt.gz · Last modified: 2020/08/21 10:14 (external edit)