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

[Mohsen Ramezanpour]

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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