Module 4 : A Case Study using Molecular Dynamics with NAMD

Lecture 19 : Steps involved in NAMD

Case Study

In this module we will study a case study on the dynamic behavior of ionic liquid : 1-butyl-3-methylimidazolium hexafluorophosphate [Bmim][PF6] (this is a green solvent and the physical properties data are very essential).We will be using the NAMD molecular dynamics package in which we will discuss the various steps required to compute the physical properties such as molar volume, isothermal compressibility and volume expansivity etc. The complete process including discussion has been adapted from:http://faculty.uml.edu/vbarsegov/teaching/bioinformatics/lectures/MDSimulationsModified.pdf) The steps involved are geometry minimization, heating, equilibration and production.We will discuss the steps involved one by one.

  1. Minimization

STEP I:  Preparation of Initial Structure

Molecular dynamics calculations are done on 125 cation i.e [Bmim] and 125 anions i.e [PF6] ( see figure 1) in a cubical cell with standard periodic boundary condition using a box size of 40 x 40 x 40 Å3.

Figure 1: Schematic of the molecule

Initial configurations were generated by randomly inserting cation-anion pairs into the simulation box. To prevent overlap, an insertion was rejected if any of the newly inserted atoms were within 1.0 Å of any existing atoms. The initial structures are generated through the use of PACKMOL [Martínez and Martínez, 2003] ( http://www.ime.unicamp.br/~martinez/packmol/) .For all the simulations, the initial cell volume was chosen to be of lower density. For [Bmim][PF6] the cubical cell of 125 cation-anion pairs is shown in Figure 2.This step includes the creation of the  PDB file (Protein Data Bank).This file stores the coordinates of all 5500 atoms in the cell. For showing the connectivity of bonds, angles, dihedrals and impropers the PSF file (Protein Structure File) is created using VEGAZZ [Pedretti et al.,2002]( http://nova.colombo58.unimi.it/cms/index.php?Software_projects:VEGA_ZZ) . The PSF, PDB and the force filed file are given in Appendix A.

Figure 2: Cubical Cell for 125 cation-anion pair of [Bmim][PF6]