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Thanks, Justin. Just one note: the values of min and max are not the same (-min -2.4750 -max 2.4750), they have opposite values. The c.o.m is taken as zero. If they were the same I would understand your suggestion, but they are not, so Gromacs should not understand that the system has zero size, should it?<br>Rebeca.<br><br><div>> Date: Sun, 11 Sep 2011 17:39:55 -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>> > Thanks again, I have uploaded to the version 4.5.4 and instead of zeros <br>> > 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 <br>> > -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 <br>> > errors. The problem comes if I assume that it is not periodic, then my <br>> > second column is "nan". In a previous mail, you had wrote me:<br>> > <br>> <br>> In what way is your channel not periodic? I'm trying to understand your problem <br>> more completely. I would suspect your issue (judging by previous commands) is <br>> that if the value of max and min are the same in the absence of -cycl, then <br>> you'll get nonsense as output. Hence I said:<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>> > <br>> > So, just to get it clear, if I assume that a system that itś not <br>> > periodic is periodic (using the option -cycl), I should have problems, <br>> > and not the opposite, what itś just what I am observing. Is it not right?<br>> <br>> I still need to know why your system isn't periodic. From before, using max = <br>> min in conjunction with -cycl gives g_wham a reasonable set of parameters to <br>> work with. Having max = min without -cycl is going to fail, because essentially <br>> you're telling g_wham that the system has zero size and therefore the reaction <br>> coordinate is of zero length (which is why, I suspect, you get "nan" - division <br>> by zero).<br>> <br>> > Besides, I have also analyzed analogous PMF results using the same <br>> > channel, but another ion (the PMF is for an ion crossing a membrane <br>> > channel), and I do not have this type of problem.<br>> > <br>> <br>> From this description, you should indeed have a periodic PMF. Thus I don't <br>> understand the insistence that -cycl shouldn't be used.<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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