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

Mark Abraham Mark.Abraham at anu.edu.au
Fri Apr 22 10:48:22 CEST 2011

On 4/22/2011 4:54 PM, majid hasan wrote:
> 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:
> http://phas.ubc.ca/~majid/Project/cntdna.mpg 
> <http://phas.ubc.ca/%7Emajid/Project/cntdna.mpg>
> My .mdp files are placed here (both .mdp files are same except for the 
> value of integrator):
> http://phas.ubc.ca/~majid/Project/lbfgs.mdp 
> <http://phas.ubc.ca/%7Emajid/Project/lbfgs.mdp>  (used for EM)
> http://phas.ubc.ca/~majid/Project/md.mdp 
> <http://phas.ubc.ca/%7Emajid/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?

#including molecule .itp files adds nothing to the system - only the 
potential to have molecule type(s). The system is defined in the 
[system] directive, and must match the corresponding coordinate file.

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

Why aren't you following a proper equilibration protocol before trying 
to make observations? You might be using position restraints, have your 
species too far apart, or simply have not simulated long enough to 
observe any movement. 200ps is an eye-blink.


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