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From: Marek Maly <marek.maly.ujep.cz>

Date: Fri, 17 Jul 2009 17:34:44 +0100

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

second one

negative charge: N2*e where e is the electron charge and N1,N2 are

natural numbers.

Let's assume that N1>N2 (overal charge is positive).

Here I have two possibilities how to neutralize given system:

#1

Add just n=N1-N2 Cl- counterions.

#2

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

this property

is rather BULK characteristic (let say characteristic of the solvent

before we put there

our polyelectrolyte molecules or the characteristic of the solvent far

enough from

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:

http://www.ks.uiuc.edu/Research/vmd/mailing_list/vmd-l/3943.html

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

counterions

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

corrections !

Best wishes

Marek

Date: Fri, 17 Jul 2009 17:34:44 +0100

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

second one

negative charge: N2*e where e is the electron charge and N1,N2 are

natural numbers.

Let's assume that N1>N2 (overal charge is positive).

Here I have two possibilities how to neutralize given system:

#1

Add just n=N1-N2 Cl- counterions.

#2

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

this property

is rather BULK characteristic (let say characteristic of the solvent

before we put there

our polyelectrolyte molecules or the characteristic of the solvent far

enough from

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:

http://www.ks.uiuc.edu/Research/vmd/mailing_list/vmd-l/3943.html

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

counterions

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

corrections !

Best wishes

Marek

-- Tato zpráva byla vytvořena převratným poštovním klientem Opery: http://www.opera.com/mail/ _______________________________________________ AMBER mailing list AMBER.ambermd.org http://lists.ambermd.org/mailman/listinfo/amberReceived on Fri Jul 17 2009 - 10:11:10 PDT

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