[gmx-users] Dynamics with DNA

Tsjerk Wassenaar tsjerkw at gmail.com
Tue May 26 08:42:53 CEST 2009

> Nearly all the force fields that can be used with Gromacs have
> nucleic acids represented as fundamental building blocks.

That may be true, but does not mean that in all these force fields the
parameters are good enough to assess 'real' behaviour of nucleic
acids. E.g. the older GROMOS force fields (43a1, 43a2, 45a3) should
not be used due to bad behaviour. Amber seems a good choice for
Protein/DNA simulations. It's not the program/package that counts,
it's the force field.



Tsjerk A. Wassenaar, Ph.D.
Junior UD (post-doc)
Biomolecular NMR, Bijvoet Center
Utrecht University
Padualaan 8
3584 CH Utrecht
The Netherlands
P: +31-30-2539931
F: +31-30-2537623

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