[gmx-users] 回复:Re: 回复:Re: Mixing rule between organic and inorganic units

[Mark Abraham]

Hi,

There's a fundamental difference between a a calculation and a simulation,
which is that the latter can defend its claim to model reality. Anybody can
put parameters into an equation.

Mark

On Mon, Aug 13, 2018, 18:49 Justin Lemkul <jalemkul at vt.edu> wrote:

>
>
> On 8/13/18 11:47 AM, Baolin Huang wrote:
> > Hi all，
> > That is a pure simulation work，no experimental data. The reviewer doubt
> the Lorentz-Berthelot combination rule for calculating the interaction
> energy between BMP-2 and HAP. I have to persuade the reviewer that the
> mixing rule works well in the BMP-2/HAP system.
>
> I understand your problem. If the reviewer doesn't believe the model,
> you have to convince them that the model works using something that is
> known, experimentally. If you don't have that, you can't convince anyone
> that your model is right.
>
> -Justin
>
> > Thanks for your help.
> > Baolin
> >
> > ----------
> > 该邮件从移动设备发送
> >
> > --------------原始邮件--------------
> > 发件人："Justin Lemkul "<jalemkul at vt.edu>;
> > 发送时间：2018年8月13日(星期一) 晚上11:31
> > 收件人："gmx-users" <gmx-users at gromacs.org>;
> > 主题：Re: [gmx-users] 回复:Re: Mixing rule between organic and inorganic units
> > -----------------------------------
> >
> >
> > On 8/13/18 11:28 AM, Baolin Huang wrote:
> >> Hi，
> >> I calculated the interaction energy（actually van der Waals part and
> electrostatic part），Rg，RMSD，and RMSF.
> >> regards，
> > I wouldn't think any of those are necessarily meaningful (interaction
> > energy almost certainly isn't, and a decomposition between vdW and
> > electrostatics definitely means nothing). Rg might be useful if there is
> > an experimental quantity with which to compare.
> >
> > The broader point is: you have to prove that your physical model
> > reproduces some known quantity before you can start making predictions
> > about others. If there's a known defect in treating energetics (which
> > should be compared with free energies of binding, etc.) then none of the
> > outcomes you generate are reliable. That seems to be your reviewer's
> > problem.
> >
> > -Justin
> >
> >> ----------
> >> 该邮件从移动设备发送
> >>
> >> --------------原始邮件--------------
> >> 发件人："Mark Abraham "<mark.j.abraham at gmail.com>;
> >> 发送时间：2018年8月13日(星期一) 晚上11:02
> >> 收件人："gmx-users" <gmx-users at gromacs.org>;
> >> 抄送："gromacs.org_gmx-users "<gromacs.org_gmx-users at maillist.sys.kth.se>;
> >> 主题：Re: [gmx-users] Mixing rule between organic and inorganic units
> >> -----------------------------------
> >> Hi,
> >>
> >> What experimental data can you replicate to show the model is valid?
> >>
> >> Mark
> >>
> >> On Mon, Aug 13, 2018, 17:34 Baolin Huang <hblin at gzhu.edu.cn> wrote:
> >>
> >>> Dear All,
> >>>      I studied the interactions between BMP-2 (protein) and
> hydroxyapatite
> >>> (HAP, inorganic material) by GROMACS with the OPLS-AA force field. The
> >>> mixing rule was the Lorentz-Berthelot combination. A reviewer commented
> >>> that 'The interaction of organic molecule on inorganic material needs
> >>> careful treatment in classical MD simulation since it is well known
> that
> >>> the mixing rule does not work well.'
> >>>      How to answer this comment? How to validate the mixing rule is
> suitable
> >>> to calculate the interaction between organic and inorganic units?
> >>>
> >>>
> >>> Best wishes,
> >>>
> >>> ------------------
> >>>
> >>> Dr. Baolin Huang
> >>> Lecturer, School of Life Sciences, Guangzhou University
> >>> --
> >>> Gromacs Users mailing list
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>
> --
> ==================================================
>
> 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
> http://www.thelemkullab.com
>
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