[gmx-users] analysis of PMF calculations

[Rebeca García Fandiño]

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:

> 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?
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.

Sorry for insisting, but I did not understand it :-S

Thanks a lot for your help.

Best wishes,

Rebeca.




> Date: Sun, 11 Sep 2011 16:33:54 -0400
> From: jalemkul at vt.edu
> To: gmx-users at gromacs.org
> Subject: Re: [gmx-users] analysis of PMF calculations
> 
> 
> 
> Rebeca García Fandiño wrote:
> > 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
> > -----------------------------------------------------------------
> > 
> 
> Upgrade to version 4.5.4 and try again.  There have been improvements to g_wham.
> 
> > 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 
> 
> Based on what your message said, I thought I understood perfectly.  Quoting:
> 
> ---
> 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"
> ---
> 
> Here everything sounds like it worked as expected and then you report the error, 
> quoting again:
> 
> ---
> /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"
> ---
> 
> Nevertheless, you should still use version 4.5.4 g_wham and report back if you 
> have problems.
> 
> -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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