Thanks Thomas That has made things a lot clearer, but just to be sure. If I pull the molecules using pull = constraints, do I still have to run umbrella sampling on the generated configurations in order to calculate the PMF? Also if I use pull_geometry = direction for the pulling can I use it for the umbrella sampling with the intention of then using g_wham for the analysis?
Many Thanks Gavin Thomas Schlesier wrote: > >> Gavin Melaugh wrote: >>> Hi All >>> >>> I am using COM pulling to pull two molecules together in order to >>> calculate the potential of mean force and the pulling is fine. I am >>> using pull = umbrella for the pulling as I am following >>> the tutorial on the website. If I use pull = constraint does this >>> still >>> pull the molecules together, and if so do you still then need to >>> perform umbrella sampling on the configurations generated? I am a >>> little >>> confused as I don't understand how the molecules pull together if they >>> are constrained. >>> >> >> For plain SMD, you can use any of the pull methods. In the tutorial >> I wrote, I explain why I used "pull = umbrella" during SMD. Umbrella >> sampling is a separate procedure, which can be done after SMD. If >> you want a free energy along the reaction coordinate, there are >> several methods for doing this, among which is umbrella sampling. >> >> -Justin >> >>> Many Thanks >>> >>> Gavin >> > > Some additions to Justins comment: > If you want to perform the umbrella sampling (or calculating the pmf > form integrating the constraint forces) it doesn't really matter how > you obtain the structures for the different windows (but you will need > them). > > If you only want to perform the calculating of the pmf, > "pull=constraint" it's a little easier to get these structures. You > can perform your pulling so that each frame of the trajectory > correspondents to one structure and then extract them from the .trr / > .xtc. Also the pulling velocity doesn't really matter. If you pull > with 1nm/ns and save the coordinates every ns, then the distance of > your molecules will increase/decrease with 1nm between the different > frames. > > If you use the same setup with "pull=umbrella" the change of the > distance won't be 1nm but will depend on "pull_k1" the spring constant > with which you're pulling. So you must "search" the structures with > the right distances (for that is Justin's Perl script). > The nice thing with "pull=umbrella" is that you can see qualitativly > what happens during the pulling. If there is somewhere a barrier in > the pmf you will see it (more or less) that the distance between the > two molecules will change slower then if the is no barrier. With lower > velocity and spring constant (pull_k1) you will see that better. > But with "pull=constraint" you won't see that. Think the best way to > understand the difference between "pull=umbrella" and "=constriant" is > that the later is the first in the limit of an infinte "pull_k1". > > Hope that helps. Good thing could be, take a small test system and > play around with the parameters and look what happens. > > Greetings > Thomas -- gmx-users mailing list [email protected] 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 [email protected]. Can't post? Read http://www.gromacs.org/mailing_lists/users.php
