Re: [AMBER] igb for non-aqueous solvent?

From: Timothy Schutt <>
Date: Mon, 1 Jun 2020 09:34:27 -0500

Thanks for the insights Dr. Case!

On Mon, Jun 1, 2020 at 9:00 AM David A Case <> wrote:

> On Fri, May 29, 2020, Timothy Schutt wrote:
> >
> >Is it an okay approximation to use igb=1 and extdiel=*dielectric value* to
> >represent a non-aqueous solvent implicitly?
> "okay" is a tough thing to answer here. Some points to consider:
> 1. Non-aqueous solvents are charactized by more than just a dieletric
> constant; with gb, changing extdiel changes way in which Coulomb
> interactions are screened. This does not capture all of the differences
> between solvent.
> 2. Amber's GB models have not been tested (much) with other solvents.
> Maybe I'm unaware of some of this work, and I hope others will chime in
> with appropriate references. So, as far as I know, one doesn't know if
> your proposed scheme will yield "reliable trends" for different
> solvents. On top of this, you are proposing a kind of hydbrid model,
> with one explicit solvent molecule and the rest being implicit; this is
> also
> likely to require careful testing.
> That said, this is research, after all. It might well work, and has
> some reasonable physics in it, especially if your solvent molecules are
> fairly small and rigid. n-octanol as a solvent would be stretch, since
> it is floppy and has both polar and non-polar parts. It's a balance
> between how much time your have and how accurate your results need to
> be.
> An alternative would be to stick with explicit solvation, and use some
> enhanced sampling method (replica exchange, self-guilded Langevin,
> perhaps one of the GaMD variants) to address the viscosity problem.
> ....good luck....dac
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Received on Mon Jun 01 2020 - 08:00:02 PDT
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