Dear lammps users,
I have a question about the simulation of proteins. I am simulating a protein using the Charmm force field. What if I don’t use a solvent? Why do people always use a solvent and water model in protein simulations ?
Best regards,
Hello,
Its not true that people always use explicit water, you can also have implicit water, which is basically vacuum + proper dielectric constant + proper thermostat for the protein (i.e. Langevin).
Whether or not the result you get with implicit water is good enough is up to you.
Simon
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Thanks for your reply. So we need to consider the effects of water using explicit or implicit water models? why do we have to do this? why we can not model the proteins individually? are the potential coefficients is written for a protein in presence of water?
It is a matter of accuracy. With explicit water, you get a much better representation of the situation since the solvation (or lack thereof) is an integral part of what determines protein behavior. Force field parameters like those in CHARMM are usually derived with respect of a specific water model, that is TIP3P in the case of CHARMM.
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