[gmx-users] analysis of PMF calculations

[Justin A. Lemkul]

Rebeca García Fandiño wrote:
> 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?

Sorry, tired eyes.  In that case, right, you have a non-zero size.

-Justin

> 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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-- 
========================================

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

========================================