Hi all Thanks for all the previous information. I have successfully pulled two molecules together in the manner that I wished. However I noticed that the two molecules both moved. I thought that only pull_group1 should move. I have searched the mailing list and stumbled upon something about removing the centre of mass motion. I do remove the centre of mass motion. To keep pull_group0 in place do you set centre of mass motion = no.
Cheers Gavin [email protected] wrote: > Sounds correct to me. One can use any method to generate the starting > conformations. Some methods may yield equilibrium starting structures > faster than other methods, but they are all ok in principle. > Nevertheless, as with any simulations, one must ensure that care is > taken to maintain equilibrium and measure convergence (unless a > non-equilibrium approach is explicitly desired). > > I also agree that people should be reading your paper -- although > maybe they are and I just misinterpreted some of the comments that I > read. Perhaps it would be less work for you if you simply put in a > line like "this tutorial is very helpful, but if you try to save an > hour and skip reading the associated paper then things are likely to > go terribly wrong somewhere!" .. and if you already have that line, > then perhaps a larger font ;) > > Chris. > > -- original message -- > > I definitely agree. I think the general point (which I know I've been > a bit > off-hand about explaining) is that, if properly applied (key caveat!), > just > about any combination of pull method + pull geometry can be used to > conduct SMD. > You're quite right that just trying to shoot some molecule across > your system > can have terrible effects for complicated environments. What I've > always meant > is that people shouldn't feel constrained to using only the settings I > have in > the tutorial, since they are not the most versatile. > > I think I'll add some discussion on this topic to my tutorial, which > seems to > have become quite popular. I guess I was hoping that people who used the > tutorial would refer to my paper (from which the tutorial is derived), > wherein > we demonstrate that our results were not influenced by the pull rate > (with both > k/2 and k/10). Maybe I should make such things more obvious :) > > -Justin > > chris.neale at utoronto.ca wrote: >> Hi guys, >> >> I just wanted to chime in on the idea that "how you perform the >> initial pulling to get structures isn't all that important" because I >> strongly disagree and think that it is, in general, immensely important. >> >> OK, it's actually not important if we're talking about pulling two >> Na+ ions, or two entirely rigid molecules in water, because you are >> not going to affect their conformations by pulling too quickly. >> However, let's take the other extreme and say that one wants to >> generate initial conformations of something in a bilayer or an ion in >> a membrane channel. In these cases, initial pulling that is too fast >> can push the bilayer, ligand, or protein so far out of its >> equilibrium conformation that your US will not sample enough >> simulation time to re-equilibrate. >> >> To sum-up my point of view, the initial pulling simulations should be >> done as slowly as you can afford, and if you want to have some >> confidence that your rate is "slow enough", then you should probably >> run at rate=k and rate=k/10 and check that the starting structures >> that you get are not separated from each other by huge barriers >> resulting from some non-equilibrium response at rate=k that was not >> observed at rate=k/10. Even if you don't go through some procedure >> like the one above, there is still no need to take risks by limiting >> your setup pulling simulation to 1 hour of simulation when you're >> going to then spend the next 2 months doing US (garbage in = garbage >> out). >> >> Chris. >> > > -- 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
