CHARMm DNA cutoffs
I am interested in gathering information about DNA simulations using
the CHARMm force field. In particular, i would like to know what cutoff
algorithms (switching vs shifting), cutoff distances (including hydrogen
bonding), etc were used. I would like to know this information for both
vacuum and solvated (especially solvated!) simulations.
I already know what is in the literature, so i don't need anything already
published. What i would like is some feedback on results, by CHARMm users,
on DNA (or relevant systems) that have not been published.
I am working with CHARMm 21.3. I would prefer information on this force field,
as the force fields in previous CHARMm versions are different. I have done
some simulations on vacuum and solvated DNA with both the switching and
shifting algorithms. I don't have the time or resources to do an
extensive analysis on the cuttoff distances for switching vs. shifting
algorithm. Along these lines, i must emphasize that i am interested
in solvated simulations!
Any input on your part would be greatly appreciated. This information
is for my own purposes---helping me decide on what parameters to use in
a DNA simulation. If there is enough input and enough interest, i will
summarize the results on the net.
wsonnen[ AT ]eagle.wesleyan.edu