Hello
I try to do molecular dynamic simulation with GROMACS software and I work on an enzyme in a plant producing a medicinal secondary metabolite. When i was searching to find a appropriate force field, i was confused. I can`t choose a force field among AMBER, CHARMM, OPLS-AA. Because all of them are used for protein MD simulation. Please give me some references and helps.
Regards
The full answer is that it depends on your system of interest: some force fields work better for intrinsically disordered proteins than others, some are better at capturing experimental observables related to protein folding of short peptides than others, etc..
In general, if you are working with a well-folded starting structure, I don't think anyone would bat an eye at choosing a common AMBER or CHARMM force field. In my work I have had good experiences with the AMBER99SB-ILDN, AMBER14SB, and new AMBER19SB/OPC water force fields.
Zahra Sadat Eslami
you should check the manual of your Software
generally, Joshua Pajak gave you interesting options
Bio+(CHARMM)
AMBER
OPLS
Hello Zahra,
Different Force Field reproduces different experimental results. The people put a lot of efforts on calculating force field parameters either using quantum chemistry or by checking how efficiently they can reproduce a particular experimental observation. Therefore, there is no unique choice. Sometimes people use two different force fields (i.e two different set of parameters) and compare results.
For simulation purpose you can go through literature to see which force field is frequently used for your protein. In general AMBER, CHARMM or OPLS are used for protein. Just be careful of the type of the force field (all atom,united atom or coarse grained). The below link may be helpful. Thank you.
http://manual.gromacs.org/current/reference-manual/functions/force-field.html
- Badges
- Science topic