summary: MD of ions in NaCl solution
- From: Marek Skowronek <mbskowro-: at :-cyf-kr.edu.pl>
- Subject: summary: MD of ions in NaCl solution
- Date: Tue, 17 Sep 1996 12:10:43 +0200 (METDST)
I am sending the summary about a molecular dynamics in NaCl solution.
I would like to thank Thomas Huber and Pascal Auffinger for their answers
that are very helpful for me.
Here is my problem that sent some weeks ago.
I have been simulating a behaviour of several molecules in water using Amber
program. However, some interesting phenomena take place in 0.9% NaCl solution.
These molecules, that are ions, have two SO3- groups which play an important
role in their interactions. I would like to take into consideration
an influence of Na+ ions in my simulations. In the Amber's manual they
suggest using CION program. I am not sure what might be the best way to do
I should be very grateful for any further comments, advice, references.
I will send the second summary as soon as possible.
Thank you in advance.
Here are the answers:
From Thomas Huber
Do you want to perform an explicit water simulation, I guess yes.
Then 0.9% NaCL = 150 mM, i.e. 1 Na+, 1Cl+ per 367 H2O.
At what concentration do you want to simulate the molecules (you said they
are ions) ?
I would say, you have to simulate a very large system, e.g. 3700 Water,
to have only some statistically meaningful answers.
Try to use a higher concentration of NaCl.
Then 2nd, you will have to include long range electrostatics. With Amber
4.1 the particle mesh ewald summation (PME) method would be ok.
Another method, neglecting longe range electrostatics, is to include
polarization of water and non-additive three body nonbonded interactions.
A paper from Peter Kollman showed the advantage of this potential. It was
some 1992 (or 91) in JACS. (Dang&Kollman ??)
From Pascal Auffinger
Please take a look at :
P. Auffinger, D.L. Beveridge,
Chem. Phys. lett. 234 - 1995 - 413-415