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<br><br>> Date: Tue, 22 Sep 2009 11:19:56 +0200<br>> From: schlesi@uni-mainz.de<br>> To: gmx-users@gromacs.org<br>> Subject: [gmx-users] Re: Re: Re: Re: Re: Re: umbrella potential<br>> <br>> Only an idea:<br>> If you start your pulling simulations (to get the windows) your spring<br>> start at some point (0.9nm?) and then moves along the pulling direction.<br>> If you now take a snapshot from the trajectory the spring is at 0.9+x nm<br>> . When you now change *only* the 'pull_rate' two things can happen:<br>> <br>> 1) 'pull_start=no' spring sits at the same point where it was at the<br>> beginning of the window-search simulation (-> force in the backward<br>> direction)<br>> -> molecule moves back and spring helps it<br>> 2) 'pull_start=yes' spring sits exactly on top of the pull_group (and<br>> isn't elongated -> no force)<br>> -> molecule moves back till the force between the two molecules and the<br>> force between the spring and the pull-molecule are equal<br>> <br>> I think the best on can do is the following:<br>> Use 'pull_start=no'. Calculate the vector from group0 to group1 -> this<br>> is then the 'pull_init'. Then make the simulations from which you get<br>> your windows. Now take the time of each window and calculate with the<br>> pull_rate the distance which the spring moved. When you now simulate a<br>> window modify 'pull_init' with this distance -> Then the spring should<br>> be exactly at the same place, in which it was in your window-search<br>> simulation.<br>> But there is probably one problem: This could (with bad luck) only work<br>> for 'position' pulling, the other pull-protocols doesn't mention the<br>> 'pull_init'.<br>> <br><br>The description of pull_init makes clear (I hope) that pull_init works<br>for all protocols (except for constant force where the is not need for it).<br><br>Berk<br><br>> One think you can check is, if the force in the window-search simulation<br>> (time when you make the snapshot) and in the window simulation (first<br>> frames) should be the same (if one neglects fluctuations).<br>> <br>> Hope this helps or gives you an idea to solve the problem.<br>> Greetings<br>> Thomas<br>> <br>> > <br>> > Ok, here is what I meant. I use each of the starting position extracted from<br>> > my original pulling trajectory (i mean the trajectory with "pull_rate =<br>> > 0.01") to simulate each window. Each of these windows still have the<br>> > umbrella force constant (pull_k1 = 35) but now have "pull_rate = 0". My<br>> > system, though, does not fluctuate about a mean position in each window. My<br>> > system returns to the initial dimer or tries to if the distance is too big<br>> > and the simulation time not long enough. So, whem I analyse the distance<br>> > between the two groups with g_dist in each of the sampling windows, I get a<br>> > series of decreasing values that will eventually return to the 0.9 nm.<br>> > For these simulations, I keep the same parameters as in the original pull<br>> > trajectory. The vectors are still the same, the force constant is still the<br>> > same. I only change the "pull_rate" from 0.01 to 0 and "pull_geometry" from<br>> > direction to distance (because g_wham asks tells me "pull_geometry =<br>> > direction" is not supported).<br>> > So maybe I am doing something wrong.<br>> > -------------- next part --------------<br>> > An HTML attachment was scrubbed...<br>> > URL: http://lists.gromacs.org/pipermail/gmx-users/attachments/20090921/82a666ca/attachment-0001.html<br>> > <br>> > ------------------------------<br>> > <br>> _______________________________________________<br>> gmx-users mailing list gmx-users@gromacs.org<br>> http://lists.gromacs.org/mailman/listinfo/gmx-users<br>> Please search the archive at http://www.gromacs.org/search before posting!<br>> Please don't post (un)subscribe requests to the list. Use the <br>> www interface or send it to gmx-users-request@gromacs.org.<br>> Can't post? Read http://www.gromacs.org/mailing_lists/users.php<br> <br /><hr />What can you do with the new Windows Live? <a href='http://www.microsoft.com/windows/windowslive/default.aspx' target='_new'>Find out</a></body>
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