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Transcript of 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
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GROMACS Introduction
GROMACS developers:
Figure: Development is a team effort, with contributors from all over the world.
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GROMACS Introduction
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:
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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
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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/
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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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GROMACS Gromcas tools
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GROMACS Gromcas tools
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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GROMACS Gromcas tools
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GROMACS Gromcas tools
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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GROMACS Gromcas tools
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GROMACS Gromcas tools
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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GROMACS Gromcas tools
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GROMACS Gromcas tools
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]
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GROMACS Working example
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GROMACS Working example
Working example
http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin/gmx-tutorials/lysozyme/
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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.
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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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