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exercises:2015_cecam_tutorial:urea

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exercises:2015_cecam_tutorial:urea [2015/08/19 14:50] – properly set chemical formulas, replace plain keywords with links to cp2k manual tmuellerexercises:2015_cecam_tutorial:urea [2020/08/21 10:15] (current) – external edit 127.0.0.1
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 Problem: QM/MM study of the Urea Zwitterion in water by means of a QM/MM Hamiltonian. Problem: QM/MM study of the Urea Zwitterion in water by means of a QM/MM Hamiltonian.
 +
 +  * Original author: Marcella Iannuzzi
 +  * Complete source and output files: [[http://cp2k.org/static/exercises/2015_cecam_tutorial/UREA.tar.xz|UREA.tar.xz]]
  
 ===== Introduction ===== ===== Introduction =====
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     &END CELL     &END CELL
     &TOPOLOGY     &TOPOLOGY
-      CONN_FILE_NAME \${ROOT}/Files/mol_solv.top+      CONN_FILE_NAME ${ROOT}/Files/mol_solv.top
       CONNECTIVITY AMBER       CONNECTIVITY AMBER
-      COORD_FILE_NAME \${ROOT}/Files/mol_solv.crd+      COORD_FILE_NAME ${ROOT}/Files/mol_solv.crd
       COORDINATE CRD       COORDINATE CRD
     &END TOPOLOGY     &END TOPOLOGY
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   &MM   &MM
     &FORCEFIELD     &FORCEFIELD
-      parm_file_name \${ROOT}/Files/mol_solv.top+      parm_file_name ${ROOT}/Files/mol_solv.top
       parmtype AMBER       parmtype AMBER
       &spline       &spline
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   &END   &END
 </code> </code>
-In the ''[[inp>FORCE_EVAL/MM/FORCEFIELD]]'' section we specify the same AMBER topology file, specified for the connectivity, since it stores the force-field information as well. In FIST (which is the classical module) the non-bonded potential is mapped on splines and in the spline section above, we specify the cutoff for these interactions (in this case 9 &#8491;).+In the ''[[inp>FORCE_EVAL/MM/FORCEFIELD]]'' section we specify the same AMBER topology file, specified for the connectivity, since it stores the force-field information as well. In FIST (which is the classical module) the non-bonded potential is mapped on splines and in the spline section above, we specify the cutoff for these interactions (in this case 9 Å).
  
 The core of the evaluation in a classical run, is the evaluation of the electrostatic. We can adjust these parameters in the ''[[inp>FORCE_EVAL/MM/POISSON]]'' section (similarly to the DFT calculations). For classical runs we can employ either standard EWALD summations, Particle-Mesh Ewald (PME) sums or Smooth-Particle-Mesh Ewald ones (SPME). The core of the evaluation in a classical run, is the evaluation of the electrostatic. We can adjust these parameters in the ''[[inp>FORCE_EVAL/MM/POISSON]]'' section (similarly to the DFT calculations). For classical runs we can employ either standard EWALD summations, Particle-Mesh Ewald (PME) sums or Smooth-Particle-Mesh Ewald ones (SPME).
exercises/2015_cecam_tutorial/urea.1439995838.txt.gz · Last modified: (external edit)