[gmx-users] DNA strands disconneting from each other along MD simulations

Justin A. Lemkul jalemkul at vt.edu
Sun May 2 18:26:02 CEST 2010

Tanos C. C. Franca wrote:
>    Hi GROMACS users !
>    I am using amber force field to perform 10 ns MD simulations of a DNA 
> dodecamer docked with small molecules in order to check if these 
> molecules stay between the strands interacting with the nucleotides, 
> but, after the simulations, I've observed that sometimes the DNA strands 
> disconnect totally from each other and some ns later get together again. 
> I initially  thought that it would be a bug of the VMD software (that I 
> used to visualize de MD results) but when I analysed the temporal RMSD 
> plots, I've saw big peaks at that times the DNA strands separated from 
> each other. Does someone knows why the DNA strands are disconneting from 
> each other and how to fix it ?

They are not disconnecting.  This behavior is a normal consequence of periodic 
boundary conditions.  Use trjconv to account for periodicity.



>    With the best regards,
>    Tanos C. C. Franca.
>    Rio de Janeiro - RJ
>    Brazil.


Justin A. Lemkul
Ph.D. Candidate
ICTAS Doctoral Scholar
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu | (540) 231-9080


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