[gmx-users] 回复:Re: 回复:Re: Mixing rule between organic and inorganic units
hblin at gzhu.edu.cn
Mon Aug 13 17:48:08 CEST 2018
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.
Thanks for your help.
发件人："Justin Lemkul "<jalemkul at vt.edu>;
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:
> I calculated the interaction energy（actually van der Waals part and electrostatic part），Rg，RMSD，and RMSF.
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
> 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
> What experimental data can you replicate to show the model is valid?
> 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
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Justin A. Lemkul, Ph.D.
Virginia Tech Department of Biochemistry
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