AMBER Archive (2004)

Subject: Re: AMBER: Implicit Solvent Models

From: David A. Case (
Date: Fri Dec 10 2004 - 10:51:12 CST

On Thu, Dec 09, 2004, Nelson Fonseca wrote:
> I want to perform some simple MD runs of of two small
> molecules solvated in hexane. To speed up the calculations
> can I use the implicit solvent model implemented in AMBER
> 8, setting the paramater relative to the dielectric
> constant equal to the value of hexane? As Im not
> interested in computing Free-energies of solvation, only
> interested in some structural information, does I need to
> scale the atomic radiis of the atoms? Is the model of GB
> suitable for non-water solvents?

The GB models in Amber have not been calibrated for non-aqueous solvents.
You could give it a try, but it is likely that structural features of small
molecules will be nearly the same in the (much cheaper) vacuum simulations.
If the difference between vacuum and hexane is really important to your study,
you may need to consider to explicit-sovlent simulations.

...good luck...dac

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