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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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Equilibration: With NVT and NPT
Temperature Equilibration
cubic box
Temperature Equilibration
rdodecahedron
Time (ps) Time (ps)
Temper
ature
(K)
Temper
ature
(K)
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Equilibration: With NVT and NPT
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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Equilibration: With NVT and NPT
Pressure Equilibration
cubic box
Pressure Equilibration
rdodecahedron
Time (ps) Time (ps)
Pressure
(bar)
Pressure
(bar)
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Equilibration: With NVT and NPT
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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