[gmx-users] More suitable force field and water model

[Mark Abraham]

Hi,

It would be miraculous if there was a good solution for all observables. A
rigid, symmetric 3-point water molecule without VDW parameters on the the
hydrogen atoms has 2 spatial, 2 charge, and 2 VDW parameters. That's not
much freedom, and most of the 6-parameter space is obviously wrong, too.
All you can do is pick a model that does something right (e.g. was the one
used to parameterize the force field), accept that your model physics is a
model, and remain alert for known and new problems. Even the quantum
chemists argue about how to model small clusters of water! ;-)

Mark



On Thu, Jun 19, 2014 at 3:55 PM, Mohsen Ramezanpour <
ramezanpour.mohsen at gmail.com> wrote:

> Dear Justin,
>
> On Thu, Jun 19, 2014 at 3:11 PM, Justin Lemkul <jalemkul at vt.edu> wrote:
>
> >
> >
> > 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.
> >
> > Yes,
> Please have a look at the abstract (
> http://www.ncbi.nlm.nih.gov/pubmed/16178604)
> and also the conclusion of (
> http://scitation.aip.org/content/aip/journal/jcp/108/24/10.1063/1.476482)
> What do you mean exactly by "something"? do you mean TIP4P does not behave
> good enough in combination with other force fields too?!
>
> >
> >  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.
>
> You are right, but some of them give more precise results and work for most
> cases! The conclusion of (
> http://scitation.aip.org/content/aip/journal/jcp/108/24/10.1063/1.476482)
>
> >
>
> >
> >> 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.
>
>
>
> Yes, I want to use this ff because of our main quantities of interest. But
> we also are interested in other quantities (for example our active site
> structure which is composed of helices, its flexibility, etc). the main
> problem I mentioned was:
> How can we rely on other quantities from our simulation while we have
> chosen some special combinations?
> No body has investigated all quantities of simulation for all ff and water
> models combinations, what can be the solution?
>
>
> >
> >
> >  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
>
>
> Some of my comments was from the same article! please have a look at the
> abstract and conclusion
>
> >
> > Thanks in advance
> > -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
> >
> > jalemkul at outerbanks.umaryland.edu | (410) 706-7441
> > http://mackerell.umaryland.edu/~jalemkul
> >
> > ==================================================
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