MOLECULAR DYNAMICS SIMULATION

Energy Minimization using GROMACS

Intro

Proteins are complex, high molecular mass, organic compounds that consist of amino acids joined by peptide bonds.

Proteins are essential to the structure and function of all living cells.

Many proteins are enzymes or subunits of enzymes. Other proteins play structural or mechanical roles, such as those that form the structures and joints of cytoskeleton. Still more functions of proteins include the storage and transport of various ligands.

In nutrition, protein serves as a source of amino acid for organisms that do not synthesize those amino acids natively.

There are also some more proteins that are pigmented in nature such as melanin.

Simulating a Protein

For the generation of a representative equilibrium two methods are available:

Monte Carlo simulations and Molecular Dynamics simulations.

For the generation of non-equilibrium ensembles and for the analysis of dynamic events, the second method is appropriate.

While Monte Carlo simulations are more simple than MD (as they do not require the computation of forces), they do not yield significantly better statistics than MD in a given amount of computer time.

Therefore Molecular Dynamics is the more universal technique for energy minimization.

Reason to perform an energy minimization is the removal of all kinetic energy from the system: if several ’snapshots’ from dynamic simulations is compared, energy minimization reduces the thermal noise in the structures and unstability, so that they can be compared better.

Molecular Dynamics Simulation

A form of computer simulation, wherein atoms and molecules are allowed to interact for a period of time under some laws of physics.

Calculates the time dependent behaviour of a molecular system.

Simulations have provided detailed information on the fluctuations and conformational changes of proteins and nucleic acids.

Used to investigate the structure, dynamics and thermodynamics of biological molecules and their complexes.

One of the principal tools in the theoritical study of biological molecules.

Significance of MD Simulation

MD simulations permit the study of complex, dynamic processes that occur in biological systems. These include, for example; Protein Stability Conformational changes Protein folding Molecular recognition: proteins, DNA, membranes,

complexes Ion transport in biological systems Drug Design Refinement of the structure determined through X-ray

Crystallography and NMR Spectroscopy.

Performing MD Simulation

To run a simulation several things are needed like: A file containing the coordinates for all atoms Information on the interactions (bond angles, charges,

Vander Waals) Parameters to control the simulation Processors to run the simulation

The PDB file contains the coordinates for all

atoms and is the input structure file for MD Simulation. The interactions are listed in the topology (.top) file and the input parameters are put into a .mdp file.

GROMACS

GROMACS (Groningen Machine for Chemical Simulations) is a molecular dynamics simulation package originally developed in the University of Groningen.

GROMACS is an engine to perform molecular dynamics simulations and energy minimization.

A high performance Molecular Dynamics Program. It is reasonably well optimized for low memory usage. The highly optimized code makes GROMACS the fastest program for

molecular simulations. The support of different force fields and the open source (GPL) character

make GROMACS very flexible. It is a high performance research tool which can be run on almost every

platform. This program is free software; it can be redistributed and/or modified under

the terms of the GNU General Public License as published by the Free Software Foundation.(A free software licence grants, to the recipients, freedoms in the form of permissions to modify or distribute copyrighted work)

Why GROMACS?

GROMACS is preferred over other Molecular Dynamics Simulation Software packages because ; It is a versatile package to perform molecular dynamics. It is user friendly, with topologies, parameter files, and error

messages written in clear text format. It provides extremely high performance compared to all other

programs. There is a lot of consistency checking. There is no scripting language. As the simulation proceeds, GROMACS continuously tells how far it

has gone, and at what time and date it is expected to be finished. Can write coordinates using compression, which provides a very

compact way of storing trajectory data. Comes with a large selection of flexible tools for trajectory analysis. GROMACS can be run in parallel, using standard MPI (Message

Passing Interface).

GROMACS File Formats

.pdb.top.itp.rtp.ndx.xvg

.mdp.tpr.edr.log.trr.xtc

Before Performing MD Simulation

Molecular Dynamics studies depend on the quality of the available experimental data. To generate an accurate minimized structure, information about its primary, secondary and tertiary structure is needed.

There are several publically available databases that contain primary, secondary and tertiary structural on proteins. Two particularly important databases are:

Protein Data Bank (PDB) at http://www.rcsb.org/pdb/. This is the primary world wide archive of structural data of biological macromolecules.

Expert Protein Analysis System (ExPASy) at http://www.expasy.ch/.This molecular biology server is dedicated to the analysis of protein sequences and structures.

The process

Running Simulation using GROMACS

Commands

Many commands are there for performing different tasks, here only mentioned the commands used for simulations.

Just type ‘–h’ to know about all commands

Simulating the protein using GROMACS involves these commands (steps)

GROMACS Flow Chart

Several steps of energy minimization may be necessary, these consist of cycles:

grompp -> mdrun.

Generating Topologies and CoordinatesGenerating Topologies and Coordinates Running a SimulationRunning a Simulation

pdb2gmx: converts pdb files to topology and coordinate files

x2top: generates a primitive topology from coordinates

editconf: edits the box and writes subgroups

genbox: solvates a system genion: generates mono atomic

ions on energetically favorable positions

genconf: multiplies a conformation in 'random' orientations

genrestr: generates position restraints or distance restraints for index groups

protonate: protonates structures

grompp: makes a run input file tpbconv: makes a run input file

for restarting a crashed run mdrun: performs a simulation

Commands

Commands (Cont.)

Many other commands are available for different tasks like=>

Viewing trajectories Processing energies Converting files Tools Distances between structures Distances in structures over time Mass distribution properties over

time Analyzing bonded interactions Structural properties Kinetic properties Electrostatic properties Protein specific analysis Interfaces Covariance analysis Normal modes

A little more details of;

pdb2gmxeditconfgenboxgromppmdrun

Changing the File Format

The pdb2gmx command converts the pdb file to a gromacs file and writes the topology.

pdb2gmx –ignh –ff [] –f [] –o [] –p [] –water spce -ignh = ignore hydrogen atoms -ff = select the forcefield -f = reads the pdb file -o = specify new pdb output file -p = output for topology file -water = uses the SPC/E water model

A Force Field is used to minimize the bond stretching energy of the molecule.

Setting up the Box for Simulations

editconf converts generic structure format to .gro, .g96 or .pdb.

editconf -bt [] –f [] –o [] –d [] -bt = mention the box type eg cubic -f = reads the pdb file -o = output -d = sets the dimension of the box

It specifies which type of box has to be used. The dimensions of the box has to be set based upon setting

the box edge approx 1.5 nm from the molecule(s) periphery. The box can be modified with options provided. The box type can be set : triclinic is a triclinic box, cubic is a

rectangular box with all sides equal dodecahedron represents a rhombic dodecahedron and octahedron is a truncated octahedron.

Adding Solvent to the Box

genbox generates a box of solvent.

genbox –cp [] –cs [] –o [] –p [] -cp = pdb input file -cs = specify water model file -o = output -p = topology input file

Adds residues at specific positions if required.The genbox command generates the solvent box

based upon the dimensions/box type that was specified using editconf.

Processing the file with Preprocessors

grompp is the pre-processor program (the gromacs pre-processor), which setups the run for input into mdrun command.

The pre-processor reads a molecular topology file, checks the validity of the file, expands the topology from a molecular description to an atomic description.

Steps performed are ; st for steepest decents cg for conjugate gradient md for molecular dynamics

Running Molecular Dynamics

Molecular Dynamics Simulation is run using mdrun.

The mdrun program is the main computational chemistry engine of MD Simulations.

mdrun produces at least three output file, plus one log file per node. The trajectory file, containing coordinates, velocities and

optionally forces. The structure file, containing the coordinates and velocities

of the last step. The energy file, contains the information about the

energies, the temperature and pressure.

Visualizing of Plots and Minimized Structure

Visualization of the trajectory file using various tools.

Generation and visualization of the plots for pressure, temperature, kinetic energy, etc.

Finding out the structure that has the minimal energy fluctuations.

Visualising this minimized structure using graphical tools.

Visualization of Plots

The generated plots can be visualized using XMGRACE.

xmgrace is a tool to make twodimensional plots of numerical data.

It runs under various flavors of Unix with X11 and M*tif (LessTif or Motif).

It also runs under VMS, OS/2, and Windows (95/98/NT/2000/XP).

Sample Plots

For Potential Energy

For Computing Root Mean Square Displacement

Visualizing Minimized Structures

DS VisualizerRasmolPymolSPDBVVMD

Sample Structures

MINIMIZED STRUCTURES OBTAINED FROM g_covar (Covariance Analysis)

Significance of Minimized Structure

Helps to find the minimal energy conformations.

Helps in better understanding of the nature of complex polymers.

Helps in better understanding of the mechanism of polymerization of proteins.

Rajendra K. LabalaScientist-1

Thank You