[gmx-users] DNA not wrapping around CNT in MD simulation

majid hasan pu_majidhasan at yahoo.com
Fri Apr 22 08:54:45 CEST 2011

Dear All,

I am doing a MD simulation of dna, and cnt in water. I get a stable simulation 
in which DNA, and CNT wiggles around there positions, but they don't seem to be 
attracted towards each other. CNT starts in the middle of the box and just moves 
a little, and DNA starts at top right corner of the box and remains there 
throughout the simulation.

movie of .trr file is here:


My .mdp files are placed here (both .mdp files are same except for the value of 
http://phas.ubc.ca/~majid/Project/lbfgs.mdp  (used for EM)
http://phas.ubc.ca/~majid/Project/md.mdp     (used for MD)

I created cnt, and dna using following commands:
For dna: pdb2gmx -f dna.pdb -o dna.gro -p dna.top -ff select (Selected 
amber99sb, and TIP3P water model)
For cnt: g_x2top -f cnt.gro -o cnt.top -ff select -pbc   (selected amber99sb)
For mixing and solvation: genbox -cp cnt.gro -ci dna.gro -o cntdna.gro -nmol 1 
-try 20 
genbox -cp cntdna.gro -cs spc.gro -o cntdnasol.gro 

In the dna.top file, amber99sb/ions.itp, and a position restraint file was also 
included along with tip3p.itp. I mentioned it because I am not sure why would it 
add ions and position restraints on adding water? 

It seems that something is wrong with non-bonded interactions, but I don't 
understand what?

Thanks for your help,
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