[gmx-users] DNA simulations

Christopher Neale chris.neale at mail.utoronto.ca
Fri Jul 6 16:16:48 CEST 2012

Hard to say if this is correct since we don't know what "resname A" is. Also, we don't know how you manually merged the DNA.

Still, you are coming back to the list too early. View your final structure in VMD and see if the ions are in the positions that you desire. Also, make a topology and a .tpr file and run an energy minimization and then a short MD simulation. Does it crash?


-- original message --

 Hello Tsjerk,

 I followed below steps to create a box with DNA and water molecules that
are close to it at some distance:

 1. g_select -s Test.gro -select '"Close to A" resname SOL and within 0.5 of
resname A' -on

   (since I need around DNA molecule, I randomly chose residue A, such that
water molecules are around A)

 2. trjconv -n index.ndx -f Test.gro -s Test.gro -o Testoutput.gro

   (Testoutput.gro - has all the water molecules that are close to the A
residue at a distance of 0.5 nm)

 3. I then merged manually the original file that has DNA molecule dna.gro
with the Testoutput.gro.

 Need some advice if I proceeded in the right direction to have a box that
has DNA + water molecules that are close to it.

 With Regards,


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