Sir i am currently pursuing my Ph.D. in biophysical chemistry (protein-ligand interaction). I have started doing docking (BEGINNER LEVEL) but i want to learn molecular dynamics simulation. Can you please let me know from where and how should i start?
Start with the books first such as;
1) The Art of Molecular Dynamics Simulation by D. C. Rapaport .
2)Computer simulation of liquids by D. J. Tildesley and M.P. Allen.
3)Understanding Molecular Simulation: From Algorithms to Applications Daan Frenkel
4)Biomolecular Simulations in Structure-Based Drug Discovery by Francesco L. Gervasio, Vojtech Spiwok, et al.
5)Computational Methods to Study the Structure and Dynamics of Biomolecules and Biomolecular Processes by Adam Liwo
6)Molecular Dynamics Simulations by Maria Emilova Velinova
7)Molecular Dynamic Simulation Studies by Vijay Raj Bollapalli and V. Raghavendra Rao Morusupalli
Also find some good review articles on Molecular Dynamics and force fields.
Download and install Gromacs
Read the Gromacs Documentation and try to understand the file preparation and force fields etc.
Take a beginner start using Justins' lab tutorial: http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin/gmx-tutorials/lysozyme/01_pdb2gmx.html
There are several software's you can try. Most of the software's are based on Linux Platform and requires GPU for maximum performance.
1) GROMACS -http://www.mdtutorials.com/index.html
2) Desmond- https://www.youtube.com/watch?v=tqt4xk_yBGs&list=PL3dxdlKx_PceAQ5FBu4WS9INVL43ybymS
3)NAMD -http://www.ks.uiuc.edu/Training/Tutorials/namd-index.html
5)AMBER- http://ambermd.org/tutorials/
6) CHARMM- https://www.charmm.org/charmm/documentation/tutorials/
You should read about molecular dynamics method first, not only follow the tutorial. when you have the basic ideas about MD, then try to do some tutorials.
Quyen V. Vu sir thank you for your insights..i will surely read the basics..is there any particular article or book which you would recommend?
Monidipa Konar I would recommend the book "Understanding Molecular Simulation" of Frenkel-Smit for simulation technique and "Protein Physics"
Justin has an excelent tutorial for begginers http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin/gmx-tutorials/lysozyme/01_pdb2gmx.html.
I reccommend you Frenkel's book as well and maybe gromacs manual
Start exploring Gromacs..Gromacs is very easy to understand at the beginner level..I used lot of molecular dynamics simulations to study protein-ligand interactions in Gromacs during my Phd..
Start with the books first such as;
1) The Art of Molecular Dynamics Simulation by D. C. Rapaport .
2)Computer simulation of liquids by D. J. Tildesley and M.P. Allen.
3)Understanding Molecular Simulation: From Algorithms to Applications Daan Frenkel
4)Biomolecular Simulations in Structure-Based Drug Discovery by Francesco L. Gervasio, Vojtech Spiwok, et al.
5)Computational Methods to Study the Structure and Dynamics of Biomolecules and Biomolecular Processes by Adam Liwo
6)Molecular Dynamics Simulations by Maria Emilova Velinova
7)Molecular Dynamic Simulation Studies by Vijay Raj Bollapalli and V. Raghavendra Rao Morusupalli
Also find some good review articles on Molecular Dynamics and force fields.
Download and install Gromacs
Read the Gromacs Documentation and try to understand the file preparation and force fields etc.
Take a beginner start using Justins' lab tutorial: http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin/gmx-tutorials/lysozyme/01_pdb2gmx.html
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