[gmx-users] analysis of PMF calculations

[Justin A. Lemkul]

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

-- 
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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

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