DSSP

There is some information about DSSP on Wikipedia. Information on the official implementations, and a copy of the original paper can be found at http://swift.cmbi.ru.nl/gv/dssp/

If you want do_dssp to run faster, you should tell it to run dssp only on frames from your trajectory that are "interesting". Usually this means a crafty choice of -b, -e and -dt options - see Online Manual: do_dssp