[gmx-users] Distribution of water polarization
rose.rhmn93 at gmail.com
Fri May 11 17:43:34 CEST 2018
On Fri, 11 May 2018, 20:04 Justin Lemkul, <jalemkul at vt.edu> wrote:
> 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:
> >>> Hi,
> >>> How can i calculate the distribution of water polarization for example
> >> for
> >>> 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)
> > 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
Sorry, i forgot to send it. The figure 2
any case I'm not going to
> have time to look into it.
Ok, but i sent... It maybe useful for someone. ;)
> 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.
Thank you so much for your detailed answer.
> Justin A. Lemkul, Ph.D.
> Assistant Professor
> 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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