[gmx-users] Re: DNA simulations

SatyaK mail2mvskumar at yahoo.com
Wed Jul 4 16:28:59 CEST 2012

 Thanks Mark for your response. These are steps I followed to construct
DNA+Water molecules.                                                                                                                                                                           
    ----> editconf -f A.pdb -o A.gro -d 0.3                                                                                                                                                                                                                                                                                                   
    ----> genbox -cp A.gro -cs -nice -20 -o A_water.gro                                                                                                                                                                                                                                                                                         
I have not used any of the topology files (which I believed should be used
in g_select) during the construction and I am not sure of handling it. Also,
I ned to introduce some OH radicals also into the cylinder with some radius
around the DNA. Could you guide me.

With regards,


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