AMBER Archive (2009)
Subject: [AMBER] The Right Neutralization Procedure and Ionic Strength Calculation ?
From: Marek Maly (marek.maly_at_ujep.cz)
Date: Fri Jul 17 2009 - 11:34:44 CDT
Dear Amber users,
My first question is related to neutralization procedure.
Let's assume that I would like to simulate complexation of two
charged molecules where the first one has positive charge: N1*(-e) and
negative charge: N2*e where e is the electron charge and N1,N2 are
Let's assume that N1>N2 (overal charge is positive).
Here I have two possibilities how to neutralize given system:
Add just n=N1-N2 Cl- counterions.
Add N1 Cl- counterions and N2 Na+ counterions.
Both above mentioned procedures guarantee neutrality of the system although
#2 is more close to reality and thus probably more suitable also for Amber
calculations am I right ?
My second question is related to ionic strength (IS).
Let's consider just IS of NaCl in our solution. So first of all, if I am
not wrong the ionic strength
should comprise just additional NaCl molecules (not the counterions) since
is rather BULK characteristic (let say characteristic of the solvent
before we put there
our polyelectrolyte molecules or the characteristic of the solvent far
that charged polyelectrolytes). Am I right ?
If yes, IS could be considered here as just volume concentration of
additional salt molecules (independently on neutralization procedure) where
the reference volume (for calculation of NaCl concentration) is the overal
volume of water molecules as it is reported here:
Am I right ?
Is it in Amber (i.e. in leap) implemented some command which could be used
for the automatic calculation and addition of the suitable number of
and then also for addition of the additional NaCl molecules to obtain
predefined ionic strength ? (Some analogy of "autoionize plugin" in VMD)
Thanks to all in advance for any relevant comments, confirmations or
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