[gmx-users] Re: DNA simulations
mail2mvskumar at yahoo.com
Fri Jul 6 03:23:10 CEST 2012
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.
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