Protocol for Molecular Dynamics Simulations of Proteins

Materials and Reagents

1. Protein structure coordinates (http://www.rcsb.org/pdb/home/home.do)
   
2. Appropriate Force field (A force field describes physical systems as collections of atoms kept together by interatomic force, e.g., chemical bonds, angles etc. [Meller, 2010]).
   
3. Molecular geometry file(.gro)
   
4. Molecular topology file(.top)
   
5. Parameter files (.mdp) (http://manual.gromacs.org/online/mdp.html)
   

Equipment

Note: In general, MD simulations require parallel computing to be able to run longer simulations in a shorter period. For smaller jobs/preprocessing, a desktop workstation machine preferably running on Linux is sufficient. However, it is preferable to perform initial steps on a local machine and final md run on a computer cluster.

1. A desktop PC with configuration below was used for initial setup of simulations :
1. HP Pavilion Desktop Intel 4 Core(TM) i5-4570 CPU@3.2GHz each
   
2. 16 GB memory
   
3. 1 TB HDD
   
4. NVIDIA GeForce GT 625
   
5. Ubuntu V15.04
   
2. The basic configuration of the supercomputer is as follows:
   
   1. Site: Center for Development of Advanced Computing (C-DAC)
      
   2. Cores: 30,056
      
   3. Memory: 14,144 GB
      
   4. Processor: Xeon E5-2670 8C 2.6GHz
      
   5. Operating System: CentOS
      
   6. MPI: Intel MPI
   Note: For the final production md run, all the jobs performed in this study were submitted to supercomputing facility at C-DAC. The resources were allocated based on the availability & requirement.
   

Software

1. Gromacs MD simulation suite v 5.1, (Abraham et al., 2015; Pronk et al., 2013; Van der Spoel et al., 2005)
   
2. Rasmol (http://www.bernstein-plus-sons.com/software/rasmol/README.html) for molecular visualization
   
3. Text editor, Gedit 3.18 (to edit the PDB file, update topology files and to edit the input run parameter files)
   
4. 2D plotting program Grace (http://plasma-gate.weizmann.ac.il/Grace) (for visualization )
   
5. Win SCP (to transfer files to and fro)
   
6. SSH client/Putty (to execute the commands on a remote server from our desktop)
   

Procedure