Gmx Slides

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Indroduction to GROMACSGROningen MAchine for Chemical Simulations

Mara Jochum

Johannes Gutenberg-Universitat Mainz

17.10.2013

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GROMACS Introduction

High performance package to perform Molecular Dynamics

Used for simulating biological (Proteins, lipids, etc.) andnon-biological(Polymers) systems

Comes with a large selection of tools for trajectory analysis

Interfaces to Quantum Chemistry and Bioinformatics/databases

Project leaders: Erik Lindahl, David van der Spoel, Berk Hess

17.10.2013 Johannes Gutenberg-Universitat Mainz Mara Jochum 3

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GROMACS developers:

Figure: Development is a team effort, with contributors from all over the world.


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GROMACS developers:

Figure: Development is a team effort, with contributors from all over the world.

GROMACS users:

... enough said, lets get started!


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GROMACS Force-fields

Force-fields I

Collection of functions and parameters which describe all particleinteractions

Types: all atom (AA), united atom (UA), coarse-grained (CG)

Examples: AMBER, CHARMM, GROMOS, OPLS, etc.


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GROMACS Force-fields

Force-fields II

Used to construct potential energies:

bondednonbonded

U= 4

r

12

r

6

+ Q1Q240r

+12

bonds

krij(rij req)2 +1

2

angles

kijk(ijk eq)2 +1

2

torsions

kijkl(1 + cos(mijkl m))

r

r ijkl

rij ijk

Can calculate forces by differentiating the potential energies:


GROMACS M l l d i

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GROMACS Molecular dynamics

Molecular dynamics

Each particle must satisfy Newtons equations of motion:

Can propagate system in space and time by integrating Newtons

equations of motion

Algorithms for integration: Leap-frog, Velocity-verlet, etc.

Can simulate in different ensembles: NPT, NVT, NVE


GROMACS T l

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GROMACS Topology

Topology

Provides a complete description of interactions between allparticles in a given system

Types: System topology (.top) Inlcude topology (.itp)

Residue topology (.rtp) Force-field .itp and .rtp files for integrated force-fields can be

found at: $ cd /PATH/TO/GROMACS/share/gromacs/top

.top file can be generated via gromacs tool pdb2gmx

.top file can be generated/downloaded with/from AutomatedTopology Builder(for gromos force-fields only):http://compbio.biosci.uq.edu.au/atb/


GROMACS G t l
http://compbio.biosci.uq.edu.au/atb/http://compbio.biosci.uq.edu.au/atb/

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GROMACS Gromcas tools

pdbgmx

Reads a coordinate file (.pdb) as well as force-field files togenerate a gromacs coordinate file (.gro) and a topology (.top)

Mostly used for large molecules with repeating residues

Relies on [ RESNAME ] entry to be present in the .rtp file

For an arbitrary molecule, you must create your own [ RESNAME ]

entry (in .rtp but better in local .top)



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editconf

Manipulates a coordinate file

Mostly used to: Define a simulation box Apply rotations, translations

Orient a solute within the simulation box

make ndx

Generates a gromacs index (.ndx) file

Contains definitions for groups of atoms for gromacs analysistools, its graphics program (ngmx), and preprocessor (grompp)



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genbox Mostly used to add solvent to a coordinate file

Can also insert molecules into a system (Options: -ciand -nmol).

genion Used to add ions to the system

Specify molecule names of ions (Options: -pname and -nname) Needs a gromacs run input .tpr file (see next slide...)



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grompp Gromacs preprocessor

Reads .top file and checks validity (naming, order, etc.)

Reads parameters (number of steps, timestep, cutoff, etc.) forthe molecular dynamics program mdrun from .mdp file

Creates a binary gromacs run input (.tpr) file for mdrun



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mdrun

Performs molecular dynamics simulations

Can also perform Brownian dynamics, and Langevin dynamics,steepest descents (energy minimization), replica exchange, etc.

To run in parallel over N processors, use:$ mpirun -np N mdrun mpi [options]


GROMACS Working example

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GROMACS Working example

Working example

http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin/gmx-tutorials/lysozyme/


GROMACS Exercise I
http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin/gmx-tutorials/lysozyme/http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin/gmx-tutorials/lysozyme/

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GROMACS Exercise I

Hexane (UA description)

System setup and equilibration:1. Using the template provided for you, fill in the topology for

hexane. How many bonds, angles, and dihedrals are needed?

2. For each of the following steps, write down the gromacscommand (with options):

Center the hexane molecule in a cubic simulation box of 4 nmlength.

Solvate the system (using the SPC/E water model). Equilibrate the system. In 1-2 sentences, describe what each of

the steps does and why it is necessary.

3. Plot the pressure and density of your equilibrated system overtime.


GROMACS Exercise II

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Hexane (CG description)Assume an MD simulation has been performed for the atomistic systemwhich you have just created (with an interface geomtry), as well as for a

coarse-grained version of the system. The corresponding trajectory files .xtchave been provided for you.

1. How would you create the interface configuration (conf.gro) from yourbulk system setup. Which gromacs command would you use?

2. Compare the atomistic and coarse-grained topologies. Make a list ofatom names contained in each coarse-grained bead.

3. Using VMD, take a snapshot (render and create a .png file) of thecoarse-grained system (VDW, transparent) superimposed onto theatomistic system (licorice, glossy).

4. Plot and compare the density profiles of the coarse-grained andatomistic simulation (as a function of the zcoordinate).

5. Similarly, plot and compare the end-to-end distances over time. Writea script to plot the distributions as a function of distance.


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