# [gmx-users] analysis of PMF calculations

Rebeca García Fandiño regafan at hotmail.com
Sun Sep 11 23:58:32 CEST 2011

```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?
Rebeca.

> Date: Sun, 11 Sep 2011 17:39:55 -0400
> From: jalemkul at vt.edu
> To: gmx-users at gromacs.org
> Subject: Re: [gmx-users] analysis of PMF calculations
>
>
>
> Rebeca García Fandiño wrote:
> > 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
> > 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):
> >
> > "For cyclic or periodic reaction coordinates (dihedral angle, channel PMF
> > without osmotic gradient), the option -cycl is useful. g_wham will make use
> > of the periodicity of the system and generate a periodic PMF. The first and
> > the last bin of the reaction coordinate will assumed be be neighbors."
> >
> > 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:
> >
>
> In what way is your channel not periodic?  I'm trying to understand your problem
> more completely.  I would suspect your issue (judging by previous commands) is
> that if the value of max and min are the same in the absence of -cycl, then
> you'll get nonsense as output.  Hence I said:
>
> >> 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.
> >
> >
> > 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?
>
> I still need to know why your system isn't periodic.  From before, using max =
> min in conjunction with -cycl gives g_wham a reasonable set of parameters to
> work with.  Having max = min without -cycl is going to fail, because essentially
> you're telling g_wham that the system has zero size and therefore the reaction
> coordinate is of zero length (which is why, I suspect, you get "nan" - division
> by zero).
>
> > 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.
> >
>
>  From this description, you should indeed have a periodic PMF.  Thus I don't
> understand the insistence that -cycl shouldn't be used.
>
> -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
>
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