Tutorial 12. MD simulation of organic nanoparticles
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T12. MD simulation of organic nanoparticles
PURPOSE: In this tutorial, it is described how to prepare isolated (non-periodic) simulation boxes that include either free or solvated nanoparticles of small organic molecules.
REFERENCE to main manual: Sections 5.5 (Excbox), 5.6 (Nanosolv), 8.9 (Nanocut), plus Sections referenced in Tutorials T3, T7, T10 and T11.
FILES: You can find all the files you need to run this tutorial here:
pyridcut.dat, pyrid.top, nano.top, meohmco.dat, meohmc.pri, meoh.top, meoh.sla.
The starting .dat trajectory file of pyridone has been produced in Tutorial T10. You will also need macros to run Excbox, Nanosolv, Nanocut and the analysis routines discussed in Tutorial T11. Place .dat files and pertinent (Windows/Unix) macros into your working directory.
The Tutorial consists of four different exercises. First, we will build a model for liquid methanol,
following the instructions given in Tutorials T3 and T7 (you can skip this part if you feel
confident with the Monte Carlo procedure). Second, we will simulate and analyze an isolated
nanoparticle of pyridone. Third, we will compute the same nanoparticle embedded in a cubic
nanodroplet of methanol. Finally, we will soak the same nanoparticle in a roughly spherical
nanodroplet of methanol. The step-by-step procedure is illustrated from scratch.