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

Mark Abraham Mark.Abraham at anu.edu.au
Fri Apr 22 10:51:47 CEST 2011

On 4/22/2011 6:48 PM, Mark Abraham wrote:
> 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.

Actually, you simulated 20ps. Your MD timestep is 0.2fs, which is 
unreasonably short. 100,000 of them is far too short to see anything happen.


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