[gmx-users] Dynamics with DNA

Justin A. Lemkul jalemkul at vt.edu
Tue May 26 02:46:16 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 ?

It is certainly possible using 3.3.2, but it would be much better to use the 
current version 4.0.5, for the most up-to-date features and *much* faster 

The choice of force field is up to you based on the simulations already 
performed and reported in the literature, as well as an examination of the force 
field derivations to determine which you feel is best suited to this purpose. 
Nearly all the force fields that can be used with Gromacs have nucleic acids 
represented as fundamental building blocks.


>   Best whises,
>   Tanos C. C. Franca.
>   Rio de Janeiro - RJ
>   Brazil
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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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