[gmx-users] Dynamics with DNA

Mark Abraham Mark.Abraham at anu.edu.au
Tue May 26 02:45:57 CEST 2009

tanos at ime.eb.br wrote:
>   Hi folks !
>   Does someone knows how to perform Molecular dynamics simulations of 
> DNA molecules using GROMACS 3.3.2 ? Is that possible ? With forcefield 
> should I use ? If it is not possible with GROMACS does someone have a 
> suggstions of which software colud be used ?

There'd be no reason to use a version of GROMACS that's at least two 
years old for a new simulation study. Use a current one.

You can certainly do such a simulation with a variety of MD packages, 
but your choice of forcefield should be driven by the behaviour you wish 
to observe, and that choice should drive your choice of simulation 
package. There's no substitute for reading the primary literature yourself.


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