> > > > > The distances between the two structures in each of the windows are (in > nm): > > 0ps = 1.56 ; 500ps = 1.54; 1000ps = 1.56; 1500 = 1.56; 2000 = 1.52; 2500 > > = 1.65; 3000 = 1.66; 3500 = 1.77; 4000 = 1.63; 4500 = 1.62; 5000 = 1.7; > > 5250 = 1.62; 5500 = 1.6; 5750 = 1.73; 6000 = 1.85; 6250 = 1.86; 6500 = > > 1.91; 6750 = 1.84; 7000 = 1.88; 7250 = 1.82; 7500 = 1.93 ; 7750 = 2.04; > > 8000 = 2.16 ; 8250 = 2.3 ; 8500 = 2.32 ; 8750 = 2.45 ; 9000 = 2.52 ; > > 9250 = 2.5 ; 9500 = 2.62 ; 9750 = 2.65 ; 10000 = 2.66 > > There is substantial overlap and jumping back and forth (i.e., 1.56, > decrease to > 1.54, increase to 1.56, then back to 1.52, etc) in these distances, so I > think > they are not optimal for umbrella sampling. Instead of more regular > spacing in > time, I would suggest more regular spacing in terms of distance. Most > literature on the topic cites how far apart windows were in terms of > distance, > which is important for WHAM analysis. > > -Justin > > > Is there a way to do this automatically in gromacs? To extract structures from the simulation based on the distance between them?
_______________________________________________ gmx-users mailing list gmx-users@gromacs.org http://lists.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 gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/mailing_lists/users.php
