> > > Stefan Hoorman wrote: > > > > > > > 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? > > > > > > No, but you can use a script that iteratively calls g_dist on separate > structures from your trajectory (trjconv -sep). See, for example: > > http://oldwiki.gromacs.org/index.php/Making_Commands_Non-Interactive > > -Justin > > > I have a test set which is comprised of the same constituents of my real system, except the solvent (i mean, it is in vacuum. This test set I use to (as the name says) test different different parameters without having to wait too much. I know it would not serve as a very quantitative set, but even though, when I changed the force_constant of the umbrella potentia to a lower value (from 35 to 10) I got something out of the WHAM that looked more like a "rollercoaster", I little bit edgy perhaps, but at least not a downstream line like the one before. When I changed it again to 5 kJ, the graphic still looked like a rollercoaster but it differed in 1 or 2 kcal more negative than the one with 10 kJ as umbrella force constant. Perhaps, in addition to space my intervals as a function of distance, my spring constant is wrong. Does that make any sense? Ahh...by the way, the link for oldwiki is not working. I will try it later.
_______________________________________________ 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