AMBER Archive (2007)

Subject: Re: AMBER: Simulation of a charged system

From: Carlos Simmerling (carlos_at_csb.sunysb.edu)
Date: Fri Jan 05 2007 - 17:41:02 CST

yes it can neutralize the system and not use explicit ions.
Explicit counterions may be more accurate for some things, but if you do
not
fully equilibrate their positions then it may be worse to include them.
You need
to decide which is best for you based on the goals and needs of your
project..

You will likely need to read articles in the literature, not just the
email archives.
Use the Amber list to find out HOW to do things, use refereed journals
to find
out WHAT to do. At least that is my opinion.
good luck!

Kijeong Kwac wrote:

> Hello, Amber users and developers:
>
> For a simulation of a charged protein in explicit solvent using the
> PME, simulation without counter ions should be preferred to using
> counter ions?
>
> I have read in the archive that Amber provides a uniform neutralizing
> plasma to make the system neutral.
>
> Could anybody give some references about this issue?
>
> Thank you in advance.
>
>
>
> <mailto:pine994_at_naver.com>
>
>
> <http://www.naver.com>NAVER <http://www.naver.com/> Korea's No.1
> search portal <http://www.naver.com/>
> <http://www.naver.com/>
>
>

-----------------------------------------------------------------------
The AMBER Mail Reflector
To post, send mail to amber_at_scripps.edu
To unsubscribe, send "unsubscribe amber" to majordomo_at_scripps.edu