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You should also be aware that when you determine a PDF for a distance<br>constrained in 3D, you will always get a "trivial" entropy contribution<br>of -2 kT log(r), which will eventually make all curves tend downwards.<br><br>Berk<br><br>> Date: Sun, 20 Sep 2009 20:28:02 -0400<br>> From: jalemkul@vt.edu<br>> To: gmx-users@gromacs.org<br>> Subject: Re: [gmx-users] umbrella potential<br>> <br>> <br>> <br>> Stefan Hoorman wrote:<br>> > I have performed a series of umbrella sampling simulations in order to <br>> > do a WHAM analysis. The profile.xvg file I obtain is a continuous <br>> > descending line along my distance axis. There is no increase in energy <br>> > after my two structures separate. Perhaps I am doing something wrong.<br>> <br>> Sounds like it, but there's no way anyone on this list will know that unless you <br>> describe your system in greater detail - how you generated the starting <br>> configurations, how many windows you used and what distances that corresponds <br>> to, the pull parameters you've specified in your .mdp file, and anything else <br>> that might be pertinent.<br>> <br>> -Justin<br>> <br>> > Thank you<br>> > <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>> -- <br>> ========================================<br>> <br>> Justin A. Lemkul<br>> Ph.D. Candidate<br>> ICTAS Doctoral Scholar<br>> Department of Biochemistry<br>> Virginia Tech<br>> Blacksburg, VA<br>> jalemkul[at]vt.edu | (540) 231-9080<br>> http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin<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 />See all the ways you can stay connected <a href='http://www.microsoft.com/windows/windowslive/default.aspx' target='_new'>to friends and family</a></body>
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