Tutorial 10. Molecular Dynamics simulation of crystals (pyridone)
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T10. Molecular Dynamics simulation of crystals (pyridone)
PURPOSE: In this tutorial, it is described how to prepare and equilibrate the P21212 RT phase of pyridone with the Molecular Dynamics technique.
REFERENCE to main manual: Sections 5.4 (Pretop); 6.2 (construction of molecular frameworks); 7.6.1 (mdmain); 7.6.2 (instruction file, .mdi); 7.6.3 (input box file, .dat); 7.6.4 (topology and force field file, .top).
FILES: You can find all the files you need to run this tutorial here: PYRIDO11.cif and pyrd.mdi. The starting structure file for pyridone (PYRIDO11.cif) has been downloaded from the Cambridge Structural Data Centre. You should produce a valid .oeh file, as well as a preliminary static energy analysis, as described in Tutorials T1 and T4. This means that you have to launch in sequence Retcif, Retcor, Retcha and Crysaa: you can do this directly with the available macro run.cry (see below). You will also need macros to run Pretop, Boxcry and mdmain. Place .cif files and pertinent (Windows/Unix) macros into your working directory.