On 6/19/14, 5:59 AM, Mohsen Ramezanpour wrote:
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.
This is actually very straightforward. Every force field was parametrized using a certain water model. That's the one you use unless there is clear evidence that a different model works better for some reason. There are very few deviations from the original parametrizations of which I am aware, and most improvements are only small.
As I understood, the SPC and TIP4P are recommended for biomolecular simulations and some authors have also recommended SPC.
Without context, there's not much value to that statement. On their own, some water models reproduce certain bulk properties better than others, but no water model is perfect. If you were to combine TIP4P with Gromos or something, I'd say that's probably unsound, even if TIP4P is "better" in terms of whatever you've chosen to look at.
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.
That's not necessarily true; I've seen demonstrations of other combinations yielding very good hydration free energies.
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.
If you're using Gromos96 53a6, it is known to produce helical instability. So the hydration free energies may be good, but the structure of the protein may suffer from artifacts.
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.
dx.doi.org/10.1021/jp0641029 -Justin -- ================================================== Justin A. Lemkul, Ph.D. Ruth L. Kirschstein NRSA Postdoctoral Fellow Department of Pharmaceutical Sciences School of Pharmacy Health Sciences Facility II, Room 601 University of Maryland, Baltimore 20 Penn St. Baltimore, MD 21201 jalem...@outerbanks.umaryland.edu | (410) 706-7441 http://mackerell.umaryland.edu/~jalemkul ================================================== -- 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.
