apresentação modsim

8/3/2019 apresentao modsim

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Molecular Dynamics

with GROMACS 4.5.5Simulation of Lysozyme Protein in Water

Work made by:

Filipe Silva pg 18990

Ricardo Oliveira pg 19002


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Main goals

Generate and analyze the topology of Lysozyme;

Define simulation box and solvate;

Add ions to nullify the system charge;

Energy Minimization of the solvated system;

Equilibration: With NVT and NPT;

Production Molecular Dynamics Simulation;

Results analysis;


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Generate and analyze the topology

of LysozymeLysozyme (1AKI) from Protein Data-

Bank

Processed lysozyme (without water

residues)


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Generate and analyze the topology

of LysozymeExecute:

pdb2gmx to obtain a structure and a topology file;


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Define simulation box and solvate

Lysozyme in a cubic box Lysozyme in a rhombicdodecahedron box

editconf to define dimentions and the box type (cubic or rhombic

dodecahedron in this case);

genbox to fill the previously generated box with HOH (solvent);


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Add ions to nullify the system charge

Grompp to generate the input file .tpr for genion;

Genion to add CL ions to counter change of the system;


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Energy Minimization of the solvated

system grompp to generate a .tpr file to run an energy minimization

simulation;

qsub to submit a script file like this:


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Energy Minimization of the solvated

system

Energy Minimization

cubic box

Energy Minimization

rdodecahedron

Time (ps)Time (ps)

Epot.(KJmol-1)

Epot.(KJmol-1

)

g_energy to visualize Potencial Energy (KJ/mol) vs Time (ps).


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Equilibration: With NVT and NPT

Equilibration is conducted in two phases

First phase is conducted under an NVT ensemble for over 100 ps at

(constant Number of particles, Volume, and Temperature)

Grompp will generate .trp file for mdrun to equilibrate the temp

of the system

g_energy will create a file that can be visualized in gnuplot.


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Temperature Equilibration

cubic box

Temperature Equilibration

rdodecahedron

Time (ps) Time (ps)

Temper

ature

(K)

Temper

ature

(K)


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Secund phase is conducted under and NPT ensemble at (constant

Number of particles, Pressure, and Temperature)

Grompp will generate .trp file for mdrun to equilibrate the

pressure of the system

g_energy will create a file that can be visualized in gnuplot


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Pressure Equilibration

cubic box

Pressure Equilibration

rdodecahedron

Time (ps) Time (ps)

Pressure

(bar)

Pressure

(bar)


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Density Equilibration

cubic box

Density Equilibration

rdodecahedron

Time (ps) Time (ps)

Dens

ity(kgm-3)

Density(kgm-3)


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Production Molecular Dynamics

Simulation grompp - to generate a .tpr for mdrun.

qsub submited a script file: -This Molecular Dinamic simulated 1 ns;


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After protein simutation, our results must be analised:

trjconv, is used for processing the coordinates

g_rms, for generate .xvga and analyses on is correctedtrajectory

Analyse the root-mean-square deviation (nm) vs Time

(1ns), for the crystal struture and crystal reference;

g_gyrate, to analyse radius of gyration of the protein

Visualize all data and


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3 of 3 Steps

RSMD

Crystal struture

cubic box

RSMD

Crystal struture

rdodecahedron

Time (ns) Time (ns)

RSM

D(nm)

RS

MD

(nm)


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3 of 3 Steps

RSMD

Crystal reference

cubic box

RSMD

Crystal reference

rdodecahedron

Time (ns)

Time (ns)

RSMD

(nm)

RSM

D

(nm)


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3 of 3 Steps

Radius of gyration

Cubic box

Radius of gyration

rdodecahedron

Time (ps)Time (ps)

Rg

(nm)

RSM

D

(nm)


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conclusions

Rhombic dodecahedron box is more appropriate for

this type of sistems, because it reduces the number of

solvent molecules to simulate;

Simulation time is lower with the use of more numberof cores;

To visualize 1ns off the interactions betwen

Time is spent with comunication betwen nodes;


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Thank you for yourattention !!!

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