Re: how to add ions to a system

From: jose correa (
Date: Wed Jan 28 2009 - 06:48:03 CST

Dear Mageshwari
I think that adding the Na ions do not make any protein conformational
changes, however, durin the MD, could be possible, particularly, if the Na
can bind to protein. You can add ions by MD, this ( can help you. You
MD in vacuum, i think that do not requires periodic boundary.
Best wishes
J Correa-Basurto
ESM-IPN, Mexico

2009/1/28 uma mageshwari <>

> hello sir,
> I am running molecular dynamics for protein-dna
> complex(nucleosome). In the log file it is mentioned that the total
> charge=-150e. I think that i have to add some sodium ions to make my system
> neutral.
> 1.will the addition of sodium ions cause any structural/functional
> disturbances?
> 2.Can u tell me how to add ions to system?
> 3.Is there any need to include periodic boundary conditions while studying
> dynamics in vacuum.

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