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Hi,<br>thanks a lot for your quick answer...<br>However, when I try the options you suggest for -cycl/nocycl, the 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>Besides, I think you have misunderstood me. When I use the option -cycl YES it's when I obtain the second column with zeros. I am working with a channel inserted into a membrane, but it is not exactly symmetric, this is why I would like to see the results obtained not using the option -cycl yes in Gromacs.<br><br>Any suggestion?<br><br>Thanks again for your help.<br><br>Best wishes,<br><br>Rebeca.<br><br><br><div>> Date: Sun, 11 Sep 2011 15:55:34 -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>> Justin A. Lemkul wrote:<br>> > <br>> > <br>> > Rebeca García Fandiño wrote:<br>> >> Hello,<br>> >> I have some old calculations (Umbrella Sampling) carried with Gromacs <br>> >> 3.3.3 and I would like to analyze them using Gromacs 4.<br>> >> When I use:<br>> >><br>> >> /GROMACS/4.5/32/bin/g_wham -bins 100 -temp 300 -tol 0.0001 -min <br>> >> -2.4750 -max 2.4750 -o pmf_1_cycl.xvg -hist histogram_cycl.xvg -ip <br>> >> ./pdo-files.dat -cycl yes<br>> >><br>> >> I get a curve with no errors, however if I don't use the option "-cycl <br>> >> yes"<br>> >><br>> > <br>> > FYI, this syntax is wrong. Boolean options are -cycl/-nocycl. They do <br>> > not take arguments.<br>> > <br>> >> /GROMACS/4.5/32/bin/g_wham -bins 100 -temp 300 -tol 0.0001 -min <br>> >> -2.4750 -max 2.4750 -o pmf_1_no_cycl.xvg -hist histogram_no_cycl.xvg <br>> >> -ip ./pdo-files.dat<br>> >><br>> >> I get a profile where the second column is all "zero"<br>> >><br>> > <br>> > 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.<br>> > <br>> >> The last lines of the analysis are (just in case it helps...):<br>> >> (...)<br>> >> 54700) Maximum change 1.204571e-02<br>> >> 54800) Maximum change 1.318242e-02<br>> >> 54900) Maximum change 1.235132e-02<br>> >> 55000) Maximum change 1.802996e-02<br>> >> 55100) Maximum change 1.166826e+00<br>> >> 55200) Maximum change inf<br>> >> 55300) Maximum change 3.161195e-01<br>> >> 55400) Maximum change 3.437561e-01<br>> >> 55500) Maximum change inf<br>> >> Switched to exact iteration in iteration 55501<br>> >> Converged in 55508 iterations. Final maximum change 0<br>> >><br>> >> I have tried to change to use the option "auto" to determine min and <br>> >> max automatically, I have also tried to remove the tolerance (and set <br>> >> the default), but the result was the same, I always obtain zero in the <br>> >> second column without the option -cycl yes.<br>> > <br>> > Again, this would be incorrect syntax. The option "-cycl auto" does not <br>> > exist.<br>> > <br>> <br>> Sorry, read that wrong. The -auto option certainly exists, but the point still <br>> stands regarding the use of -cycl and its purpose.<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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