[gmx-users] Re: DNA simulations

SatyaK mail2mvskumar at yahoo.com
Fri Jul 6 03:23:10 CEST 2012

 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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