[gmx-users] corrupted lines in alchemical

Thu Jul 21 23:36:49 CEST 2016

On 7/21/16 5:33 PM, Alexander Alexander wrote:
> 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?
>

Check the contents of md.xvg for each window.  If you have lambda-coupled 
restraints, you'll have an energy contribution from them in that file, along 
with anything else that was perturbed.  pullx.xvg and pullf.xvg are just the 
default output from the pull code whenever you use it; it has nothing to do with 
this particular free energy calculation.

-Justin

> 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
>>>>
>>>> ==================================================
>>>> --
>>>> Gromacs Users mailing list
>>>>
>>>> * Please search the archive at
>>>> http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before
>>>> posting!
>>>>
>>>> * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
>>>>
>>>> * For (un)subscribe requests visit
>>>> https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or
>>>> send a mail to gmx-users-request at gromacs.org.
>>>>
>>>>
>> --
>> ==================================================
>>
>> 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
>>
>> * Please search the archive at
>> http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before
>> posting!
>>
>> * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
>>
>> * For (un)subscribe requests visit
>> https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or
>> send a mail to gmx-users-request at gromacs.org.
>>

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

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

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