[gmx-users] corrupted lines in alchemical

[Alexander Alexander]

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.

Regards,
Alex