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

Justin Lemkul jalemkul at vt.edu
Mon Aug 13 17:31:21 CEST 2018

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 


> ----------
> 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
>> --
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Justin A. Lemkul, Ph.D.
Assistant Professor
Virginia Tech Department of Biochemistry

303 Engel Hall
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