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Yes,<br>my profile seems normal, the only problem are the units in the x-axis, because I expected them to be in the range of the dimensions of the channel.<br>I will try if I see differences with the other options you proposed, anyway.<br>Thanks a lot for your help!!<br>Best wishes, <br>Rebeca.<br><br><div><div id="SkyDrivePlaceholder"></div>> Date: Thu, 31 May 2012 15:52:48 -0400<br>> From: jalemkul@vt.edu<br>> To: gmx-users@gromacs.org<br>> Subject: Re: [gmx-users] Re: boundaries in PMF<br>> <br>> <br>> <br>> On 5/31/12 3:51 PM, Rebeca García Fandiño wrote:<br>> > OK,<br>> > however, just one point about your last comment:<br>> ><br>> > > I suspect this is why g_wham is finding a range of values only equal to half of<br>> > > your expected reaction coordinate; it is considering only the positive<br>> > > displacement along the reaction coordinate.<br>> ><br>> > It seems like all the channel is explored, not only one half. If g_wham was only<br>> > considering the positive displacement I should see a profile for just one half<br>> > of the channel, shouldn´t I? and I can see a profile typical for the entire channel.<br>> ><br>> <br>> Then perhaps it's just a small g_wham output bug (boundary values). You didn't <br>> mention that your profile looked normal ;)<br>> <br>> -Justin<br>> <br>> -- <br>> ========================================<br>> <br>> Justin A. Lemkul, Ph.D.<br>> Research Scientist<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/Support/Mailing_Lists/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/Support/Mailing_Lists<br></div> </div></body>
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