Euston, Stephen R wrote: > Hi, > > > > I am hoping to use essential dynamics to look at unfolding of proteins > (probably barley lipid transfer protein and bovine beta-lactoglobulin). > I have searched the Gromacs database, and the web but I can find very > little info on the actual process of running the simulation. I have also > looked at the WHAT IF home page, and again I can’t seem to find much > here either. Does anyone know of a web tutorial or other that covers > essential dynamics simulations? > > >
make_edi -h gives some coarse info with a number of references. there are also still a number of slides online that sketch the way the different constraint algorithms work: http://www.mpibpc.gwdg.de/groups/de_groot/presentations/edsam/ for protein unfolding you may also consider conformational flooding, which is implemented in gromacs as well: again make_edi -h or http://www3.interscience.wiley.com/cgi-bin/abstract/112750179/ABSTRACT cheers, Bert ______________________________________ Bert de Groot, PhD Max Planck Institute for Biophysical Chemistry Computational biomolecular dynamics group Am Fassberg 11 37077 Goettingen, Germany tel: +49-551-2012308, fax: +49-551-2012302 http://www.mpibpc.mpg.de/groups/de_groot _______________________________________________ gmx-users mailing list gmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to [EMAIL PROTECTED] Can't post? Read http://www.gromacs.org/mailing_lists/users.php
