Molecular dynamics simulations

with GROMACS

Virtual Simulation Lab

07.04.2016
 Molecular dynamics
Newton's second law

F=ma

F=−∇ V (r )

Bridge between micro- and macroscopic

and between theory and experiment
Allen 2004

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 Force field

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 Force field

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 Statistical ensamble
NPT NVT μVT

Microcanonical (NVE) ensemble

Canonical (NVT) ensemble

Isothermal-isobaric (NPT) ensemble

Grand canonical (μVT) ensemble

NVE NVT μVT

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 GROMACS

Free under GNU Lesser General Public License

Constant development

Well documented

Among the fastest MD codes

User-friendly

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 How to install GROMACS
Linux
sudo apt-get install gromacs
Download it from http://www.gromacs.org/Downloads

Windows
http://www.gromacs.org/Downloads/Installation_Instructions/Windows

http://jenkins.gromacs.org/

Avogadro
sudo apt-get install avogadro Visualization and
http://avogadro.cc/wiki/Main_Page molecular editing
tools
Visual Molecular Dynamics (VMD)
http://www.ks.uiuc.edu/Research/vmd/
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 Steps to run MD simulation
Create molecule - avogadro
Create topology - topolgen
gmx insert-molecules
gmx solvate
gmx grompp
gmx genion
Prepare your system

gmx grompp
gmx mdrun
Energy minimization
gmx energy

gmx grompp
Equilibration run gmx mdrun

Production run gmx grompp

gmx mdrun

Analysis gmx make_ndx

gmx rdf
gmx hbond

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 Files in
GROMACS

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 Files in
GROMACS

Molecule coordinates

Molecule topology

Parameter file

System topology

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 Files in GROMACS

Geometry files - *.gro, *.pdb

Index and name

of the residue
Atom name
Name
and number Atomic coordinates

Number of
atoms

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 Files in GROMACS
Topology files - *.top and *.itp

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 Files in GROMACS
Input file with MD parameters - *.mdp

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 Ready to give it a try?

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