[gmx-users] corrupted lines in alchemical

[Justin Lemkul]

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

==================================================