[gmx-users] corrupted lines in alchemical
Alexander Alexander
alexanderwien2k at gmail.com
Thu Jul 21 23:34:34 CEST 2016
Why not? For each lambda for me from 0 to 21, one md.xvg and two pull.xvg
have been produced, and alchemical analysis go through these file for each
lambda and collect the data for free energy and derivative of free energy
..., actually the pull.xvg files are not only zero, what I bought above is
just an example for Lambda = 0, and the problem here is not with the Zero.
I need to indicate the portion of each perturbation in the free energy
change, but what alcehemical now gives me is just the portions of vdW and
coulom and the restraints portion is missing.
What is that single file, please? And how I can drive the portion of each
perturbation from that single file?
Thanks.
Regards,
Alex
On Thu, Jul 21, 2016 at 11:17 PM, Justin Lemkul <jalemkul at vt.edu> wrote:
>
>
> On 7/21/16 4:36 PM, Alexander Alexander wrote:
>
>> Hi,
>>
>> VERSION 5.1.2 single precision.
>>
>>
> The pullx.xvg and pullf.xvg files shouldn't factor into any analysis, in
> any case. So even though mdrun wrote all zeroes, you shouldn't need those
> files. All the perturbed terms are written to a single file. Those are
> what you need to process.
>
> -Justin
>
>
> 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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> --
> ==================================================
>
> 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
>
> ==================================================
> --
> Gromacs Users mailing list
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