> The cations should end up very close to the DNA solute anyway, since they
> will be attracted by the phosphates.
Well, not necessarily all of them. According to Manning's counterion
condensation theory (that have stood the test pf time pretty well) only
about 75% of the counterions are within ca 10 A of the DNA.
Mihaly Mezei,
Dept. of Physiology & Biophysics, Mount Sinai School of Medicine
Voice: (212) 241-2186 Fax: (212) 860-3369|
WWW: http://
adsr13.mssm.edu/domains/dept/facultyInfo.epl?objname=physbio&user=mezeim01
From rajaamber6_at_rediffmail.com 21 Feb 2001 09:24:22 -0000
Message-id: <20010221092422.7633.qmail.mailweb22.rediffmail.com>
Date: 21 Feb 2001 09:24:22 -0000
From: Raja Swaminathan <rajaamber6_at_rediffmail.com>
To: AMBER list <amber.heimdal.compchem.ucsf.edu>
Subject: weights for DNA and ions
In-Reply-to: <200102122142.QAA24661.pop.uky.edu>
hi
i am doing MD on a DNA duplex. in the first stage of minimization weights are given only to DNA (amber tutorial) and not the ions. does it cause any problem because equilibration of water may take away the ions out of the scene.
is it advisable to constrain both DNA as well as ions in the first stage itself
thanks
raja
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Received on Tue Feb 20 2001 - 14:18:45 PST
