CHARMM and AMBER are the force fields used in the computational simulation for the properties of dna, protein, etc. I'd like to know that, when to use CHARMM or AMBER force field. Also is it necessary to do MD Simulation via both of them.
Thank You.
There is no idea to help you know which foce field is better. the both force fields are wildley used. The study on how these force fields serve and also comparing them on your systems and the consistency with the experiments are out of the scope of your project. Instead of asking which one is good, it’s better to focus on force field functions.
no one is allowed to ask you why you selected amber and not charmm in your project.
I should say that the bases and the sources of many force fields are OPLS force field.
People believe CHARMM forcefield is better for proteins while AMBER forcefiled is better for DNA simulations. I think force field are parameterised optimally for different molecular groups.
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Furthermore, there seems to have no any noticeable difference between the force fields like AMBER, CHARMM, GROMACS, GROMOS, etc used in computational biophysics after going through all this:
https://en.wikipedia.org/wiki/Comparison_of_software_for_molecular_mechanics_modeling
https://www.flickr.com/photos/softsimu/6929028590
https://www.researchgate.net/post/Is_AMBER_or_CHARMM_force_field_better_for_protein_structural_biology_studies
https://www.youtube.com/watch?v=AtDOJnVNC18
https://www.quora.com/In-Molecular-Dynamics-why-there-are-different-force-fields-AMBER-CHARMM-GROMOS-etc
https://pubs.acs.org/doi/abs/10.1021/acs.jcim.5b00308?journalCode=jcisd8
Article Insights on P-Glycoprotein's Efflux Mechanism Obtained by Mo...
Article Comparison of the AMBER, CHARMM, COMPASS, GROMOS, OPLS, TraP...
Article Comparison of Protein Force Fields for Molecular Dynamics Simulations
The force field is an important "part" of molecular simulations indeed. Its choice may affect the conclusions severely. Unlike @Ramin, I do think that it is perfectly valid to ask, why you chose a certain force field or not another one. The conclusions should always be checked, where they are force-field independent.
CHARMM and AMBER force fields differ in many aspects and also at various levels. For instance, the atomic charges were derived differently. The differences are not only in between the force field families, but also within them. For instance for proteins, Amber03 is different than Amber12 or Amber99, and it is not straightforward to say, which one is the best.
Practically, I would recommend you to read articles which validate/compare force fields of your type of biomolecule and process of interest. You should, in ideal case, validate your choice of force field yourself on a set of experimental (or higher level theory calculations) data. However, the situation if often not so hopeless. The force field selection depends on the level of detail you require in your study. You would need a highly accurate force field to capture a subtle conformational change or a single hydrogen bond which would be the major conclusion of the study. On the other hand perhaps, a less accurate force field would be fine for simulations of larger-scale conformational changes which would complement e.g. biochemical experiments.
Here I put a few references where to start:
folded proteins:
https://doi.org/10.1371/journal.pone.0032131
https://doi.org/10.1016/j.bpj.2011.03.051
disordered proteins:
https://doi.org/10.1038/nmeth.4067
https://doi.org/10.1021/acs.jctc.5b00736
nucleic acids:
https://doi.org/10.1038/nmeth.3658
https://doi.org/10.1021/acs.jctc.6b00186
https://doi.org/10.1021/ct501025q
membranes:
https://doi.org/10.1021/acs.jctc.7b00001
https://doi.org/10.1007/s00232-010-9296-8
@ Michal H. Kolář thank you for your perfect article advices. it really helped me.
Michal H. Kolář There is much literature about protein etc. But how to decide which force filed to choose if you have chemical molecules like surfactants or a mixture of organic compounds ( present in crude oil from petroleum sources)
Neetish Kumar Maurya There are universal force fields for organic molecules, drug-like molecules, ionic liquids and others. A quick Google search should give you some answer. OPLS might suit you in your case.
original all-atom: https://doi.org/10.1021/2Fja9621760
most recent: https://doi.org/10.1021/acs.jctc.5b00864
I also recommend a paper by Caleman et al. about simulating organic liquids, where you can catch a feel about how accurate results you might expect. https://doi.org/10.1021/ct200731v
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