[gmx-users] DNA simulations

Mark Abraham Mark.Abraham at anu.edu.au
Sun Jul 1 12:07:51 CEST 2012

On 1/07/2012 7:31 AM, SatyaK wrote:
>   Hello All,
>   I am working on DNA simulations using GROMACS
> Question: I created A.gro file that has DNA molecule and water molecules
> within a box using GROMACS. I want to create a cylinder around the DNA so
> that I can place some ions, or, compute axis of DNA so that I can place ions
> closely to it. Could you guide me on the same.

You can define a special set of water molecules that are candidates for 
replacement with genion, and let it choose them randomly. Read the -h 
output for genion and editconf carefully, and note that the special set 
must be contiguous in the coordinate file. So maybe use g_select to 
define the special set according to some geometric criterion, two runs 
of editconf to create coordinate files with respectively the special set 
removed and just the special set, concatenate them with a text editor 
(being sure to follow all the file format details) so the special set is 
now contiguous, adjust the .top to have two different solvent groups and 
finally use genion.


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