[gmx-users] analysis of PMF calculations

Justin A. Lemkul jalemkul at vt.edu
Sun Sep 11 23:39:55 CEST 2011

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 A. Lemkul
Ph.D. Candidate
ICTAS Doctoral Scholar
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu | (540) 231-9080


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