From the MD-related questions I have received over emails and on the 3DNA forum, I sense that users do not have that much of a problem or inconvenience in applying 3DNA for the task. There is one issue that does stand out, however, i.e., the use of find_pair for each and every structure in the trajectories to prepare an input file that contains base-pairing information for analyze to calculate various parameters. As an example, a recent article by Ricci et al., "Molecular Dynamics of DNA: Comparison of Force Fields and Terminal Nucleotide Definitions" (J Phys Chem B. 2010 Jul 8. [Epub ahead of print]), says that:
It is noteworthy that, because the DNA structure endured strong deformations in these simulations, 3DNA could not perform the analysis of the angles for all the 5000 snapshots. Actually, for system 3 the calculation of the backbone parameters could be performed in only 59% of the snapshots, whereas in system 4 only 18% of the configurations allowed this calculation.Dr. Netz, the corresponding author, confirmed to me that:
I don't think this is a 3DNA problem, but is rather an effect of the distortion caused by the problems in parameterization of the GROMOS forcefield.Essentially, though, the problem lies in the coupled use of find_pair/analyze; for strongly deformed DNA structures along the simulation trajectories, some base pairs melt out, and are thus beyond the recognition of find_pair. On the other hand, one does not need to run find_pair for each structure; simply prepare a template input file for analyze, with the help of find_pair and probably some manual editing, then all the structures can be analyzed, no matter how distorted they are. Furthermore, saving the find_pair step should speed up the analysis of thousands of structures, typical of MD simulations.
In fact, 3DNA (from v1.5) has a Perl script named nmr_strs that implements the above idea in a preliminary form. The script is intended to serve as a starting point for the analysis of multiple similar structures, in an NMR ensemble or from MD simulations. See 3DNA wiki page on nmr_strs for details.
In the long run, a better integration between 3DNA and AMBER or other MD packages would solve this problem from the upstream, thus making users' life (downstream) much easier. Until that happens, I hope this post could help clarify the issue somewhat in this important application area of 3DNA. As always, I greatly value your comments.