[gmx-users] DNA simulations

Christopher Neale chris.neale at mail.utoronto.ca
Wed Jul 4 16:51:59 CEST 2012

Mark's suggestions were complete. However, you did not follow them. Please follow all of his suggestions
and then post back with exactly what you did and exactly what problem you ran into. If you are having
trouble with g_select, then show us what you did and why it didn't work. The mailing list should be used
in addition to, not as a substitute for, reading the manual and testing it out yourself.


-- original message --

 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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