[gmx-users] corrupted lines in alchemical

[Alexander Alexander]

Hi,

VERSION 5.1.2   single precision.

Regards,
Alex

On Thu, Jul 21, 2016 at 10:07 PM, Justin Lemkul <jalemkul at vt.edu> wrote:

>
>
> On 7/21/16 3:09 PM, Alexander Alexander wrote:
>
>> Dear gromacs user,
>>
>> In free energy perturbation calculation by alchemical analysis for my
>> system in which the restraints-lambda by pull code, columb and vdW have
>> been applied. After convergence, I applied "alchemical_analysis -p prd. -u
>> kcal", but immediately many corrupted files are detected as below;
>>
>> ++++++++++
>>    Line #1 (got 6 columns instead of 4)
>>     .
>>     .
>>     .
>>     .
>>
>>     .
>>     .
>>     Line #60011 (got 6 columns instead of 4)
>>     Line #60012 (got 6 columns instead of 4)
>>     Line #60013 (got 6 columns instead of 4)
>>     Line #60014 (got 6 columns instead of 4)
>>     Line #60015 (got 6 columns instead of 4)
>>   warnings.warn(errmsg, ConversionWarning)
>> Traceback (most recent call last):
>>   File "/usr/bin/alchemical_analysis", line 9, in <module>
>>     load_entry_point('alchemical-analysis==1.0.2.dev0', 'console_scripts',
>> 'alchemical_analysis')()
>>   File
>>
>> "/usr/lib/python2.7/site-packages/alchemical_analysis-1.0.2.dev0-py2.7.egg/alchemical_analysis/alchemical_analysis.py",
>> line 1207, in main
>>     nsnapshots, lv, dhdlt, u_klt = parser_gromacs.readDataGromacs(P)
>>   File
>>
>> "/usr/lib/python2.7/site-packages/alchemical_analysis-1.0.2.dev0-py2.7.egg/alchemical_analysis/parser_gromacs.py",
>> line 188, in readDataGromacs
>>     removeCorruptLines(f,f)
>>   File
>>
>> "/usr/lib/python2.7/site-packages/alchemical_analysis-1.0.2.dev0-py2.7.egg/alchemical_analysis/utils/corruptxvg.py",
>> line 105, in removeCorruptLines
>>     raise DataRemovalError
>> Exception: 60019 corrupted lines of 60029 found, that is more than 10.0
>> percent. Removal failed, examine input file  ./prd.0_pullf.xvg
>>
>> +++++
>> The corrupted files are with files produced out of restraints as I when
>> discard the prd._pullf.xvg and prd._pullx.xvg and apply the alchemical, it
>> works fine.
>> Here also is the header of one of the prd.0_pullf.xvg file, I do not know
>> where are the extra columns that cause problems.
>>
>> +++++++
>> #   gmx_mpi mdrun -ntomp 1 -deffnm prd.0 -s prd.0
>> # gmx mdrun is part of G R O M A C S:
>> #
>> # Getting the Right Output Means no Artefacts in Calculating Stuff
>> #
>> @    title "Pull force"
>> @    xaxis  label "Time (ps)"
>> @    yaxis  label "Force (kJ/mol/nm)"
>> @TYPE xy
>> @ view 0.15, 0.15, 0.75, 0.85
>> @ legend on
>> @ legend box on
>> @ legend loctype view
>> @ legend 0.78, 0.8
>> @ legend length 2
>> @ s0 legend "1"
>> @ s1 legend "2"
>> @ s2 legend "3"
>> @ s3 legend "4"
>> @ s4 legend "5"
>> 0.0000  -0      -0      -0      -0      0
>> 0.1000  0       -0      0       0       -0
>> 0.2000  0       0       0       0       -0
>> 0.3000  0       -0      -0      -0      -0
>> .
>> .
>> .
>> .
>> ++++++++
>>
>> Thanks for your comments.
>>
>>
> I remember this being a bug in an old version.  What GROMACS version did
> you use for the simulations?
>
> -Justin
>
> --
> ==================================================
>
> Justin A. Lemkul, Ph.D.
> Ruth L. Kirschstein NRSA Postdoctoral Fellow
>
> Department of Pharmaceutical Sciences
> School of Pharmacy
> Health Sciences Facility II, Room 629
> University of Maryland, Baltimore
> 20 Penn St.
> Baltimore, MD 21201
>
> jalemkul at outerbanks.umaryland.edu | (410) 706-7441
> http://mackerell.umaryland.edu/~jalemkul
>
> ==================================================
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