Hi, thanks a lot for your quick answer... However, when I try the options you suggest for -cycl/nocycl, the program indeed ask for arguments:
------------------------------------------------------- Program g_wham, VERSION 4.5 Source code file: statutil.c, line: 338 Fatal error: Expected a string argument for option -cycl ----------------------------------------------------------------- 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. Any suggestion? Thanks again for your help. Best wishes, Rebeca. > Date: Sun, 11 Sep 2011 15:55:34 -0400 > From: [email protected] > To: [email protected] > Subject: Re: [gmx-users] analysis of PMF calculations > > > > Justin A. Lemkul wrote: > > > > > > Rebeca García Fandiño wrote: > >> Hello, > >> I have some old calculations (Umbrella Sampling) carried with Gromacs > >> 3.3.3 and I would like to analyze them using Gromacs 4. > >> When I use: > >> > >> /GROMACS/4.5/32/bin/g_wham -bins 100 -temp 300 -tol 0.0001 -min > >> -2.4750 -max 2.4750 -o pmf_1_cycl.xvg -hist histogram_cycl.xvg -ip > >> ./pdo-files.dat -cycl yes > >> > >> I get a curve with no errors, however if I don't use the option "-cycl > >> yes" > >> > > > > FYI, this syntax is wrong. Boolean options are -cycl/-nocycl. They do > > not take arguments. > > > >> /GROMACS/4.5/32/bin/g_wham -bins 100 -temp 300 -tol 0.0001 -min > >> -2.4750 -max 2.4750 -o pmf_1_no_cycl.xvg -hist histogram_no_cycl.xvg > >> -ip ./pdo-files.dat > >> > >> I get a profile where the second column is all "zero" > >> > > > > That makes sense. You're telling g_wham that you have a PMF starting > > and ending at the same place, but it's not a periodic profile. It can't > > debias the sampling windows over zero space. > > > >> The last lines of the analysis are (just in case it helps...): > >> (...) > >> 54700) Maximum change 1.204571e-02 > >> 54800) Maximum change 1.318242e-02 > >> 54900) Maximum change 1.235132e-02 > >> 55000) Maximum change 1.802996e-02 > >> 55100) Maximum change 1.166826e+00 > >> 55200) Maximum change inf > >> 55300) Maximum change 3.161195e-01 > >> 55400) Maximum change 3.437561e-01 > >> 55500) Maximum change inf > >> Switched to exact iteration in iteration 55501 > >> Converged in 55508 iterations. Final maximum change 0 > >> > >> I have tried to change to use the option "auto" to determine min and > >> max automatically, I have also tried to remove the tolerance (and set > >> the default), but the result was the same, I always obtain zero in the > >> second column without the option -cycl yes. > > > > Again, this would be incorrect syntax. The option "-cycl auto" does not > > exist. > > > > Sorry, read that wrong. The -auto option certainly exists, but the point > still > stands regarding the use of -cycl and its purpose. > > -Justin > > -- > ======================================== > > Justin A. Lemkul > Ph.D. Candidate > ICTAS Doctoral Scholar > MILES-IGERT Trainee > Department of Biochemistry > Virginia Tech > Blacksburg, VA > jalemkul[at]vt.edu | (540) 231-9080 > http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin > > ======================================== > -- > gmx-users mailing list [email protected] > http://lists.gromacs.org/mailman/listinfo/gmx-users > Please search the archive at > http://www.gromacs.org/Support/Mailing_Lists/Search before posting! > Please don't post (un)subscribe requests to the list. Use the > www interface or send it to [email protected]. > Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
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