[gmx-users] Re: DNA simulations

Tsjerk Wassenaar tsjerkw at gmail.com
Thu Jul 5 09:30:07 CEST 2012

Hi Satya,

You can use trjorder to rearrange solvent molecules in your structure
file, according to distance. Then you can replace the first x solvent
molecules by hydroxyl. Actually you only need to remove a hydrogen
atom per water...

Hope it helps,


On Thu, Jul 5, 2012 at 5:04 AM, SatyaK <mail2mvskumar at yahoo.com> wrote:
>  Thanks once again Mark. I am trying to figure out things. Basically, I am
> using ReaxFF for my simulations. The basic problem I want to address is, to
> place OH radicals as close as possible to the DNA and rest with water
> molecules in a box.
>  Thanks,
>  Satya.
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Tsjerk A. Wassenaar, Ph.D.

post-doctoral researcher
Molecular Dynamics Group
* Groningen Institute for Biomolecular Research and Biotechnology
* Zernike Institute for Advanced Materials
University of Groningen
The Netherlands

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