[gmx-users] Distribution of water polarization
jalemkul at vt.edu
Fri May 11 17:34:13 CEST 2018
On 5/11/18 11:29 AM, rose rahmani wrote:
> On Fri, 11 May 2018, 19:38 Justin Lemkul, <jalemkul at vt.edu> wrote:
>> On 5/11/18 11:06 AM, rose rahmani wrote:
>>> How can i calculate the distribution of water polarization for example
>>> the first two layers of water at the solid surface?
>>> How about the number of water molecules with a given polarization?
>>> I mean exactly figure2 of this article.
>>> Can gmx dipoles do it?
>> Did you do a polarizable simulation?
> No, it is sth like calculating the distribution of polarization (dipole) in
> different dimensions separately. Sth like different orientation of water
> molecules which cause to different orientations of dipoles in different
> dimensions. (Hope to explain clearly, if it's possible please take a look
> at the article)
There is no article, nothing linked, but in any case I'm not going to
have time to look into it.
If you've done a classical, nonpolarizable MD simulation, you can make
no claims about polarization. You could compute properties related to
water molecule orientation (e.g. gmx hydorder), which will tell you
about the dipole moment orientation in the context of a fixed triangle
of charges, but that's all you're going to get from simulations like
these. FWIW, in reality, the dipole moment of the water molecules will
not be exactly related to these fixed geometries, so this is a weak
comparison, in my mind.
Justin A. Lemkul, Ph.D.
Virginia Tech Department of Biochemistry
303 Engel Hall
340 West Campus Dr.
Blacksburg, VA 24061
jalemkul at vt.edu | (540) 231-3129
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