Re: how to add ions to a system/DASHOFSALT

From: Thomas C. Bishop (bishop_at_tulane.edu)
Date: Wed Jan 28 2009 - 09:10:23 CST

1) the ions are absolutely necessary and in case of nucleosome biologist
know that even the type of ions makes a difference.

2) I once contributed a script called DashOfSalt.vmd
at
http://www.ks.uiuc.edu/Research/vmd/mailing_list/vmd-l/att-4723/DashOfSalt.vmd

it replaces bulk water with pairs of ions.

An updated version is at
http://dna.ccs.tulane.edu/~bishop/VMD/DashofSalt.v2.vmd

(I used it this past week and seems to work)

It was originally developed for nucleosome simulations
(Bishop JBSD 2005)

3) in vacuum. my vote is NO but others may differ.

4) for nucleosome simulations I have a series of tools and scripts
that can take you from initial download of xray structure all the way
thru system building and equilibration.
It can wrap ANY sequence of DNA onto any nucleosome xray structure.

Let me know if you'd like to help me perfect these tools.
or are interested in using some of them.

Tom

On Wed, 2009-01-28 at 14:48 +0530, uma mageshwari wrote:
> 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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