Dear Gromacs Users, I have read some articles about the more appropriate combination of force field and water model for different simulations of interest. It is confusing and too difficult to decide which combination is the best one. Besides according to articles I read, I am in doubt now and not sure which combination should I choose.
As I understood, the SPC and TIP4P are recommended for biomolecular simulations and some authors have also recommended SPC. Although SPC/E seems the best one in non-polarizable models for bulk properties of water but for different quantities of interest such as hydration free energy, hydration enthalpy, entropy, heat capacities etc. some special combinations will be more appropriate. I found that although using a FF+water model will result in a precise enough quantity but we can not rely on some other quantities of our simulation! By this I mean, If we are interested in hydration free energy, the best option seems to be Gromos 53a6 and SPC or SPC/E model. But if we are interested in other quantities as well, other combinations will be preferred. In fact I am interested in Protein-ligand binding free energy and also its Enthalpy and Entropy contributions as well. I guess in this case it is better to choose Gromos+SPC or SPC/E. But I am not sure. I think it is also related to properties of our system components (charge, etc.). for example for sugars or lipids. Is there any article which has compared these in details? Please let me know. any suggestion is appreciated in advance Best Regards -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org.