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

[Justin Lemkul]

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
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> --------------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
340 West Campus Dr.
Blacksburg, VA 24061

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