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--- exercises:2018_uzh_acpc2:mol_sol [2018/05/08 11:07] – [Water] jglan
+++ exercises:2018_uzh_acpc2:mol_sol [2018/05/08 11:12] – [Ramachandran plot] jglan
@@ Line 4: / Line 4: @@
 [[http://www1.lsbu.ac.uk/water/water_models.html|Water molecular models]] are computational techniques that have been developed in order to help discover the structure of water. In this section, you will be asked to calculate some physical properties based on classical molecular dynamics simulation. The TIP3/Fw model will be usded in the simulations.
-We have prepared a CP2K input file ''water.inp'' for running a MD simulation of liquid water using the force field from the first exercise (parametrized by [[https://aip.scitation.org/doi/pdf/10.1063/1.1884609|Praprotnik et al.]]). Download {{ water.zip |water.zip}}
+We have prepared a CP2K input file ''water.inp'' for running a MD simulation of liquid water using the force field from the first exercise (parametrized by [[https://aip.scitation.org/doi/pdf/10.1063/1.1884609|Praprotnik et al.]]).
+<note important>Download {{ water.zip |water.zip}}</note>
@@ Line 85: / Line 86: @@
 Visualize the structure ''glyala.pdb'' with VMD and determine the atomic indices of the atoms defining the dihedral angles.
 </note>
+<note important>The index number in VMD is different from the number in CP2K, as the index start from 0 in VMD, 1 in CP2K. Thus, one need to specify index number + 1 obtained from VMD</note>
 With this knowledge at hand,