T7. Monte Carlo: simulation of a liquid flexible molecule (n-pentane)
PURPOSE: In this tutorial, it is described how to prepare and equilibrate a liquid box of normal-pentane with the Monte Carlo technique. The aim is to get the user acquainted with the use of slave atoms for the Monte Carlo routine of MiCMoS.
REFERENCE to main manual: Sections 5.2 (Boxliq); 5.4 (Pretop); 6.2 (construction of molecular frameworks); 6.6.1 (mcmain); 6.6.2 (instruction file); 6.6.3 (topology and force field file); 6.6.4 (slave atom file).
FILES: You can find all the files you need to run this tutorial here: pentane.mci, pentane.oih, pentane.sla, pentane.top. The starting point is the pentane.oih structure file, which can be prepared by using Retcor as a molecule builder, as detailed in Tutorial T3. File pentane.mci contains the MC running commands. You will also need macros to run individual modules Retcor, Retcha, Pretop, Boxliq and mcmain. Place .oih and pertinent (Windows/Unix) macros into your working directory.
