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Thanks again, I have uploaded to the version 4.5.4 and instead of zeros in the second column, I obtain nan, which comes to be the same :-S<br>Sorry, but I am a bit confused about your comments. If I use the option -cycl (this is what I can read in the Help from Gromacs):<br><br>"For cyclic or periodic reaction coordinates (dihedral angle, channel PMF<br>without osmotic gradient), the option -cycl is useful. g_wham will make use<br>of the periodicity of the system and generate a periodic PMF. The first and<br>the last bin of the reaction coordinate will assumed be be neighbors."<br><br>If I assume that my channel is periodic (which it is not), I do not get errors. The problem comes if I assume that it is not periodic, then my second column is "nan". In a previous mail, you had wrote me:<br><br><pre>> That makes sense. You're telling g_wham that you have a PMF starting <br>> and ending at the same place, but it's not a periodic profile. It can't <br>> debias the sampling windows over zero space.</pre><br>So, just to get it clear, if I assume that a system that itś not periodic is periodic (using the option -cycl), I should have problems, and not the opposite, what itś just what I am observing. Is it not right?<br>Besides, I have also analyzed analogous PMF results using the same channel, but another ion (the PMF is for an ion crossing a membrane channel), and I do not have this type of problem.<br><br>Sorry for insisting, but I did not understand it :-S<br><br>Thanks a lot for your help.<br><br>Best wishes,<br><br>Rebeca.<br><br><br><br><br><div>> Date: Sun, 11 Sep 2011 16:33:54 -0400<br>> From: jalemkul@vt.edu<br>> To: gmx-users@gromacs.org<br>> Subject: Re: [gmx-users] analysis of PMF calculations<br>> <br>> <br>> <br>> Rebeca García Fandiño wrote:<br>> > Hi,<br>> > thanks a lot for your quick answer...<br>> > However, when I try the options you suggest for -cycl/nocycl, the <br>> > program indeed ask for arguments:<br>> > <br>> > -------------------------------------------------------<br>> > Program g_wham, VERSION 4.5<br>> > Source code file: statutil.c, line: 338<br>> > <br>> > Fatal error:<br>> > Expected a string argument for option -cycl<br>> > -----------------------------------------------------------------<br>> > <br>> <br>> Upgrade to version 4.5.4 and try again. There have been improvements to g_wham.<br>> <br>> > Besides, I think you have misunderstood me. When I use the option -cycl <br>> > YES it's when I obtain the second column with zeros. I am working with a <br>> <br>> Based on what your message said, I thought I understood perfectly. Quoting:<br>> <br>> ---<br>> When I use:<br>> <br>> /GROMACS/4.5/32/bin/g_wham -bins 100 -temp 300 -tol 0.0001 -min -2.4750 -max <br>> 2.4750 -o pmf_1_cycl.xvg -hist histogram_cycl.xvg -ip ./pdo-files.dat -cycl yes<br>> <br>> I get a curve with no errors, however if I don't use the option "-cycl yes"<br>> ---<br>> <br>> Here everything sounds like it worked as expected and then you report the error, <br>> quoting again:<br>> <br>> ---<br>> /GROMACS/4.5/32/bin/g_wham -bins 100 -temp 300 -tol 0.0001 -min -2.4750 -max <br>> 2.4750 -o pmf_1_no_cycl.xvg -hist histogram_no_cycl.xvg -ip ./pdo-files.dat<br>> <br>> I get a profile where the second column is all "zero"<br>> ---<br>> <br>> Nevertheless, you should still use version 4.5.4 g_wham and report back if you <br>> have problems.<br>> <br>> -Justin<br>> <br>> -- <br>> ========================================<br>> <br>> Justin A. Lemkul<br>> Ph.D. Candidate<br>> ICTAS Doctoral Scholar<br>> MILES-IGERT Trainee<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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