I would like to run a MD simulation on pyrite. Which force field is suitable for this simulation?
Dear Mohammad,
Force fields for inorganic materials are pretty spotty. It may be difficult to find a reliable force field for such a material. Even the well parameterized ones tend to only work well in certain situations. Thus, it's important to know what sorts of the questions you want to solve. Do you want to study surface interactions between pyrite and biomolecules? Or are you interested in the bulk materials properties of pyrite (for example, studying dislocations in the pyrite crystal lattice)? The force field that you use will depend on your interests.
Regards,
Jeff
Dear Mohammad,
to successfully solve such a problem, I'd suggest using the conventional CHARMM software with its most recent force field of general validity.
To practically solve the problem you might wish to use the CHARMMING INTERFACE:
http://www.charmming.org/charmming/html/skeleton/
Here you might upload your actual PDB file and work with it. Please note that this WEB interface has only short computational time. But it's possible to download all the preliminary results thus obtained - and restart the simulation on the computers at your disposal.
If you need further assistance, please write me directly.
Respectfully yours,
Jewgeni
Dear Mohammad,
Force fields for inorganic materials are pretty spotty. It may be difficult to find a reliable force field for such a material. Even the well parameterized ones tend to only work well in certain situations. Thus, it's important to know what sorts of the questions you want to solve. Do you want to study surface interactions between pyrite and biomolecules? Or are you interested in the bulk materials properties of pyrite (for example, studying dislocations in the pyrite crystal lattice)? The force field that you use will depend on your interests.
Regards,
Jeff
As an accurate force field for pyrite may indeed be hard to identify, another option, depending on the resources available and the size of the systems that you want to model, would be to use ab-initio MD, which does not rely on finding an accurate forcefield. See J. Chem. Phys., 119, 4934, 2003 for an example concerning pyrite.
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