Re: Implicit solvent simulation

From: Bjoern Olausson (
Date: Fri Jul 08 2011 - 05:57:03 CDT

On Friday 08 July 2011 12:35:40 jaya c.jose wrote:
> Dear all,
> I am trying to simulate a peptide using GB-OBC implicit solvent model in
> NAMD2.8.
> My system is having total charge -5,so is it possible to use explicit ions
> to neutralize the system?
You don't need to neutralize your system.

> I would like to know what is the thumb rule to choose the ion concentration
> for a system.
Do you have lab experiments you want to match against or any information at
which ion concentration the protein is handled? If yes, I would suggest to
start with those values.

If you have no clue at all, I would say it can't harm to add ions in the range
from 1 mM to 500 mM (0M represents distilled water) but that is finally up to
you any your system... for example if you have an protein/enzyme which is
halophilic you might want to ramp up you ion concentration.

Why not run some short test simulations to see how very high/low salt
concentration affect your system.


Bjoern Olausson
Martin-Luther-Universitšt Halle-Wittenberg 
Fachbereich Biochemie/Biotechnologie
Kurt-Mothes-Str. 3
06120 Halle/Saale
Phone: +49-345-55-24942

This archive was generated by hypermail 2.1.6 : Mon Dec 31 2012 - 23:20:33 CST