AMBER Archive (2005)

Subject: AMBER: Two question about dielectric constant

From: 烨 武 (elevenren_at_yahoo.com.cn)
Date: Mon Apr 11 2005 - 03:02:10 CDT

I'm sorry to ask questions again which may be asked frequently.
I have read some letters about this items in the archive, but I am still confused about these questions, so please help!
I want to minimize a structure of a protein considering the solvent effects but excluding explicit water.
In the Frequently Asked Questions (FAQ)("http://amber.ch.ic.ac.uk/Questions/dielc.html), it said:
"In the case of excluding explicit water the distance dielectric model seems to be the most fashionable,------"
But I still have two question:
1.In this situation, when we use the distance dielectric model, which value should we choose for dielectric constant, 1 or larger,in order to model the water surrounding better?
2. In above distance dependent dielectric setting, will the software use the same dielectric constant value when computing the electrostatic interactions between two atoms separated by other protein atoms and two atoms seperated by surrounding waters (if the distance is the same)?
If it is true, I think it is unreasonable, itn't it?
Thank you for your help!
 
 
 Zheng Canhui

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