[gmx-users] Choosing water molecules and box type and dimensions

[Justin Lemkul]

On 4/29/16 9:17 AM, abhijit Kayal wrote:
> you can look the following paper for the properties of different water
> models.
>
> Simulating water with rigid non-polarizable models: a general perspective
> Phys. Chem. Chem. Phys., 2011, 13, 19663–19688.
>
> In this paper they compare all the water models based on their different
> thermodynamics and
> dynamical properties. It tuns out TIP4P/2005 water model is the best one
> which can mimic the
> bulk water most closely.
>

When simulating a protein system, the most important consideration is not bulk 
water properties, instead it is compatibility with the force field being used 
for the protein.  The water model with which the biomolecular force field was 
parametrized should always be used unless there is specific evidence for a 
different combination being superior.

-Justin

> On Fri, Apr 29, 2016 at 5:21 AM, zeineb SI CHAIB <zeineb-14 at hotmail.com>
> wrote:
>
>> Hi,
>>
>> I'm working on a protein and two cofactors and one substrate, I have too
>> simulate all this system on GROMACS. I'm in the first stage: choosing a
>> force field, box type and dimensions, water molecules...etc.
>>
>> I would like to know more about the water molecule types (I looked on the
>> internet but I didn't find much informations) (what is the difference
>> between them, according to what I should choose a type..etc) and the box
>> type and dimensions that I should choose?
>>
>> Thank you in advance for your help.
>>
>> Cordially.
>>
>> Zeineb.
>>
>>
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>
>
>

-- 
==================================================

Justin A. Lemkul, Ph.D.
Ruth L. Kirschstein NRSA Postdoctoral Fellow

Department of Pharmaceutical Sciences
School of Pharmacy
Health Sciences Facility II, Room 629
University of Maryland, Baltimore
20 Penn St.
Baltimore, MD 21201

jalemkul at outerbanks.umaryland.edu | (410) 706-7441
http://mackerell.umaryland.edu/~jalemkul

==================================================