[gmx-users] More suitable force field and water model
jalemkul at vt.edu
Thu Jun 19 15:13:37 CEST 2014
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
> 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
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
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
jalemkul at outerbanks.umaryland.edu | (410) 706-7441
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