[gmx-users] pullx.xvg format

[Justin A. Lemkul]

Gavin Melaugh wrote:
> Hi Justin
> 
> Thanks for the reply. I expanded the terminal and it didn't make a
> difference. Do you still think it's O.K?
> 

I don't see why not.  If Gromacs produced the output, you didn't change it, 
g_wham didn't produce an error, and the results weren't completely nonsensical 
or buggy, then there's no reason to panic.

-Justin

> Gavin
> 
> 
> 
> 
> Justin A. Lemkul wrote:
>>
>> Gavin Melaugh wrote:
>>> Hi all
>>>
>>> I have a very quick question. The output for umbrella pulling
>>> simulations (pullx.xvg) often appears to have an irregular format, in
>>> that the columns don't seem to be perfectly aligned (see below).
>>> I have never had a problem with this as g_wham never reported any
>>> errors. I was just wondering is this an issue?
>>>
>> It shouldn't be.  Data are parsed based on line breaks.  I imagine
>> this output might look "normal" if you expand the size of your
>> terminal to get everything on one line.
>>
>> -Justin
>>
>>> Cheers
>>>
>>> Gavin
>>>
>>> 8631.6006       1.05024 3.941   3.80205 0.0919597      
>>> 0.147718       -0.0215892
>>> 8631.9004       1.03157 3.94253 3.80054 0.0290956      
>>> 0.175955       -0.0447413
>>> 8632.2002       1.01474 3.96139 3.81348 0.0594728      
>>> 0.160099       -0.0482623
>>> 8632.5000       1.0197  3.95987 3.82872 0.0515857      
>>> 0.140793       -0.0359526
>>> 8632.8008       1.03466 3.94717 3.83522 0.0775257      
>>> 0.156349       -0.0268523
>>> 8633.1006       1.03959 3.94529 3.83996 0.0630389      
>>> 0.140153       -0.0315862
>>> 8633.4004       1.0372  3.95998 3.82624 0.0489344       0.1468 
>>> -0.0239522
>>> 8633.7002       1.02653 3.95994 3.82712 0.0632881      
>>> 0.142731       -0.0574301
>>> 8634.0000       1.01196 3.95079 3.81532 0.0594033      
>>> 0.128616       -0.057459
>>> 8634.3008       1.00748 3.93597 3.82667 0.146123       
>>> 0.114964       -0.0386781
>>> 8634.6006       1.00209 3.91869 3.83553 0.0928916      
>>> 0.119439       -0.0338013
>>> 8634.9004       0.993704        3.92392 3.8084  0.0669909     
>>> 0.152878        -0.0255926
>>> 8635.2002       1.00164 3.94898 3.79449 0.0824905      
>>> 0.170253       -0.0137497
>>> 8635.5000       1.0168  3.95829 3.78047 0.058119       
>>> 0.158457       -0.0219142
>>> 8635.8008       1.03037 3.95717 3.7914  0.0950175      
>>> 0.145733       -0.0685743
>>> 8636.1006       1.0152  3.94208 3.78807 0.0705052      
>>> 0.147887       -0.0117258
>>> 8636.4004       1.00647 3.93244 3.79199 0.092164       
>>> 0.130635       -0.00548112
>>> 8636.7002       1.02261 3.91966 3.76668 0.0743383      
>>> 0.160227       -0.0491515
>>> 8637.0000       1.0466  3.91742 3.73989 0.0766793      
>>> 0.134678       -0.09385
>>> 8637.3008       1.04931 3.93179 3.75026 0.126789       
>>> 0.115951       -0.0487055
>>> 8637.6006       1.04238 3.94086 3.73288 0.127404       
>>> 0.150352       0.00932272
>>> 8637.9004       1.02266 3.92861 3.74975 0.0541594      
>>> 0.164885       -0.0608739
>>> 8638.2002       1.01286 3.93057 3.77248 0.14425 0.10085 -0.00612713
>>> 8638.5000       1.01337 3.94557 3.79916 0.11815 0.0991607      
>>> 0.00891958
>>> 8638.8008       0.987062        3.93091 3.81182 0.0363212     
>>> 0.168897        -0.0292177
>>> 8639.1006       0.995336        3.93407 3.82284 0.122306      
>>> 0.0993002       -0.00813846
>>> 8639.4004       1.00739 3.95131 3.82143 0.0971151      
>>> 0.124606       -0.0229913
>>> 8639.7002       1.01473 3.98067 3.82504 0.130283       
>>> 0.117168       -0.0369952
>>> 8640.0000       1.02179 3.97666 3.80322 0.107674        0.13277
>>> -0.0346299
>>> 8640.3008       1.02445 3.96855 3.79499 0.0598816      
>>> 0.185437       -0.0311454
>>> 8640.6006       1.03611 3.94857 3.79149 0.105113       
>>> 0.122864       0.00836338
>>> 8640.9004       1.02776 3.94737 3.79431 0.09896 0.093913       
>>> -0.0594025
>>> 8641.2002       0.993178        3.93066 3.80311 0.0987073     
>>> 0.146735        -0.0481467
>>> 8641.5000       0.981653        3.91943 3.7912  0.0527064     
>>> 0.155903        -0.0340922
>>> 8641.8008       0.99508 3.92219 3.80137 0.112235        0.08475
>>> -0.0709295
>>> 8642.1006       1.0068  3.91384 3.78044 0.0627984      
>>> 0.156858       -0.0764401
>>> 8642.4004       1.00386 3.93476 3.80116 0.080642       
>>> 0.0993683      -0.050131
>>> 8642.7002       0.993248        3.90789 3.80662 0.0890923     
>>> 0.148829        -0.0430867
>>> 8643.0000       0.992517        3.87576 3.79073 0.091716      
>>> 0.134674        -0.0131645
>>> 8643.3008       0.995234        3.89502 3.7805  0.0704844     
>>> 0.156837        -0.0469381
>>> 8643.6006       1.01357 3.91115 3.75715 0.0796926      
>>> 0.128354       -0.0687171
>>> 8643.9004       1.01555 3.90522 3.75396 0.0917188      
>>> 0.140592       -0.0575233
>>>
> 
> 

-- 
========================================

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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