Re: MD using implicit solvent

From: Vermaas, Joshua (
Date: Fri Dec 30 2016 - 11:03:05 CST

I'm a bit unfamiliar with all the details, but isn't the dielectric
constant you set effectively set the solvent being used? So for water,
the dielectric is 80ish. Acetonitrile is 40ish. Something like
Chloroform is near 5. You just look it up in a table you trust, and off
you go. Implicit solvent models currently can't model the first or
second solvation layers that might structure around a solute, so the
dielectric determines the effective solvent.


On 12/30/2016 05:29 AM, wrote:
> Hello,
> For MD simulation I have been following the NAMD tutorials. In the midway
> I got a bit confused how should I proceed; if I have to run my simulation
> using Acetonitrile solvent implicitly. Because following the Generalized
> Born Implicit Solvent configuration file I got lost as to how to indicate
> the system about the specific solvent that is to be used.
> It would be grateful if you could help me with the script or the steps
> that I should follow.
> Thanking you in anticipation
> _Hemchandra Deka

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