Hey Tanos, You must read some papers but my recommendations are:
GMX 4.0.5 and AMBER99SB forcefield. Look at http://acpypi.googlecode.comwhere you can find info about how to add amber forcefield to GMX. Cheers, Alan Subject: [gmx-users] Dynamics with DNA > > 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 ? > Best whises, > Tanos C. C. Franca. > Rio de Janeiro - RJ > Brazil > > -- Alan Wilter S. da Silva, D.Sc. - CCPN Research Associate Department of Biochemistry, University of Cambridge. 80 Tennis Court Road, Cambridge CB2 1GA, UK. >>http://www.bio.cam.ac.uk/~awd28<<
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