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

abhijit Kayal abhijitchemiitd at gmail.com
Fri Apr 29 15:18:00 CEST 2016

you can look the following paper for the properties of different water

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.

On Fri, Apr 29, 2016 at 5:21 AM, zeineb SI CHAIB <zeineb-14 at hotmail.com>

> 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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Abhijit kayal
Research Scholar
Theoretical Chemistry
IIT Kanpur

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