Hello! I am still learning MD and found that there are different softwares that can do this job such as GROMACS, NAMD, AMBER, CHARMM, Desmond, and OpenMM. So what is the difference between them?. And if there is any review that tells the difference between the force fields (AMBER, CHARMM, and OPLS), I will be grateful.
Article Comparison of Protein Force Fields for Molecular Dynamics Simulations
Hi Ibrahim,
The difference is more significant between the force fields than in the computational package. I recommend an article that may be useful to answer your questions.
Shirts, M. R., Klein, C., Swails, J. M., Yin, J., Gilson, M. K., Mobley, D. L., ... & Zhong, E. D. (2017). Lessons learned from comparing molecular dynamics engines on the SAMPL5 dataset. Journal of computer-aided molecular design, 31(1), 147-161.
Thank you very much for this article. but what I meant is why are there many simulation softwares for MD?
edit: I get it now. you mean that the difference is in the used force field not in the used software so the softwares are the same.
For a conventional user the difference between these packages is mainly in application: each package has its own pros and cons, but as with any other tool at the end of the day what matters most is how good it fits to the specific job or problem. Some of them are more generally applicable (from organics to solid state), but require more user input, the others are more specialised, but have less requirements on users.
Thanks very much. Do you have any suggestions on which one should I use if I want to make MDS on a protein-drug system? @Vitalie Botan
It is true that you value mainly the applicability of the forcefield to the specific system, and the availability and quality of parameters for it. To decide on this the way is to look in the literature for similar systems. There are however also other factors that you might want to evaluate: is the program using a certain forcefield for free? Is it already in use in the group (so that you can get help if necessary)? What kind of computer power do you have? GPU? And then based on that you can maybe decide even better.
For proteins Amber is widely used (with Amber program) but also charmm forcefield (with namd program).
Hi Ibrahim,
I recommend you start with gromacs since it is a free licence software and more user friendly than for example Amber, and will also allow you to study the type of system in which you are interested.
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