[gmx-users] analysis of PMF calculations

[Rebeca García Fandiño]

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
-----------------------------------------------------------------

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 channel inserted into a membrane, but it is not exactly symmetric, this is why I would like to see the results obtained not using the option -cycl yes in Gromacs.

Any suggestion?

Thanks again for your help.

Best wishes,

Rebeca.


> Date: Sun, 11 Sep 2011 15:55:34 -0400
> From: jalemkul at vt.edu
> To: gmx-users at gromacs.org
> Subject: Re: [gmx-users] analysis of PMF calculations
> 
> 
> 
> Justin A. Lemkul wrote:
> > 
> > 
> > Rebeca García Fandiño wrote:
> >>  Hello,
> >>  I have some old calculations (Umbrella Sampling) carried with Gromacs 
> >> 3.3.3 and I would like to analyze them using Gromacs 4.
> >>  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"
> >>
> > 
> > FYI, this syntax is wrong.  Boolean options are -cycl/-nocycl.  They do 
> > not take arguments.
> > 
> >> /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"
> >>
> > 
> > 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.
> > 
> >> The last lines of the analysis are (just in case it helps...):
> >> (...)
> >>     54700) Maximum change 1.204571e-02
> >>     54800) Maximum change 1.318242e-02
> >>     54900) Maximum change 1.235132e-02
> >>     55000) Maximum change 1.802996e-02
> >>     55100) Maximum change 1.166826e+00
> >>     55200) Maximum change inf
> >>     55300) Maximum change 3.161195e-01
> >>     55400) Maximum change 3.437561e-01
> >>     55500) Maximum change inf
> >> Switched to exact iteration in iteration 55501
> >> Converged in 55508 iterations. Final maximum change 0
> >>
> >> I have tried to change to use the option "auto" to determine min and 
> >> max automatically, I have also tried to remove the tolerance (and set 
> >> the default), but the result was the same, I always obtain zero in the 
> >> second column without the option -cycl yes.
> > 
> > Again, this would be incorrect syntax.  The option "-cycl auto" does not 
> > exist.
> > 
> 
> Sorry, read that wrong.  The -auto option certainly exists, but the point still 
> stands regarding the use of -cycl and its purpose.
> 
> -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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