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

Justin Lemkul jalemkul at vt.edu
Mon Aug 13 17:49:30 CEST 2018

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.


> 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
>>> * Please search the archive at
>>> http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before
>>> posting!
>>> * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
>>> * For (un)subscribe requests visit
>>> https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or
>>> send a mail to gmx-users-request at gromacs.org.


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


More information about the gromacs.org_gmx-users mailing list