Re: [AMBER] Question about chemical reaction in vacuum with adding an extra reaction field (Specify dielectric constant in vacuum)

From: 王婷婷 <ttwang.mail.dlut.edu.cn>
Date: Fri, 12 Apr 2019 09:40:46 +0800 (GMT+08:00)

We've already used different explicit solvents to do the QM/MD sampling simulation for my target chemical reaction.
Now, we want to individually evaluate the effect of dielectric constant of solvents on reaction process.
Putting the reactant in vacuum with an extra reaction field (dielc=78), is that appropriate?


> -----原始邮件-----
> 发件人: "David A Case" <david.case.rutgers.edu>
> 发送时间: 2019-04-11 21:57:52 (星期四)
> 收件人: "AMBER Mailing List" <amber.ambermd.org>
> 抄送:
> 主题: Re: [AMBER] Question about chemical reaction in vacuum with adding an extra reaction field (Specify dielectric constant in vacuum)
>
> On Thu, Apr 11, 2019, 王婷婷 wrote:
> >
> >I want to evaluat the effect of polarity of organic solventon chemical
> >reaction, and I put the reactants in vacuum with an extra reaction field,
> >which set the igb=6(vacuum) and dielc=78(an extra reaction field)in
> >Amber input file.
>
> The above looks like an oversimplified model for a water environment,
> not an organic solvent. It would probably have the effect of destroying
> hydrogen bonds, and other bad effects. Using a GB model like igb=2 or
> 5 (since this is not a biomolecule) would be more likely to give good
> results.
>
> I don't think any of the Amber implicit solvent models (other than RISM
> or PBSA) should be expected to work well in organic solvents. Are you
> sure that you can't use an explicit solvent representation? A lot will
> depend on (a) how much effort you want to spend on this question; and
> (b) how much accuracy you need to get useful results.
>
> ...good luck...dac
>
>
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--
------------------------------------------------------------------------------------
王婷婷
大连理工大学工业生态与环境工程教育部重点实验室
 地址:辽宁省大连市甘井子区凌工路2号 环境楼
 邮编:116024
 电话:183-4223-5107
 Tingting Wang
 Key Laboratory of Industrial Ecology and Environmental Engineering (MOE) , CHINA
 School of Environmental Science and Technology, Dalian University of Technology Dalian, CHINA

116024,P. R.
 Phone Number: +86 183-4223-5107

 E-mail: ttwang.mail.dlut.edu.cn
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Received on Thu Apr 11 2019 - 19:00:02 PDT
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