O.K Thanks guys Gavin
Justin A. Lemkul wrote: > > > Thomas Schlesier wrote: >> For umbrella sampling you need to steps: >> 1) get the configurations for the later umbrella sampling (step 5 in >> Justins tutorial). How you perform the pulling sim. for that isn't >> important, you only need the structures. >> 2) umbrella sampling (step 6 in tutorial). Here you use the >> configurations from step 1. I think here you can only use >> "pull=distance" (i think). >> > > Both "distance" and "position" work with the WHAM algorithm. Only > "direction" is unsupported. It would be nice for this to be > officially documented (if it isn't already) so that users don't find > this out after collecting a huge amount of data that they can't > analyze. I know it's on the wiki (I put it there), but a statement in > the manual is definitely warranted. > > -Justin > >> Greetings >> Thomas >> >>> >>> 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
