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

From: David A Case <>
Date: Thu, 11 Apr 2019 09:57:52 -0400

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

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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Received on Thu Apr 11 2019 - 07:00:03 PDT
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