[gmx-users] g_covar warnings

[João Henriques]

Great, that's what I needed to know. Still, I totally agree with you. There
are certain best practices, and using a .tpr is always the best choice.

Thanks,
João


On Thu, Mar 27, 2014 at 7:02 PM, Justin Lemkul <jalemkul at vt.edu> wrote:

>
>
> On 3/27/14, 1:54 PM, João Henriques wrote:
>
>> Thanks Justin. That corroborates my "no .tpr, no party" suspicion.
>> However,
>> would it be possible to achieve a correct analysis if I were to use a
>> whole
>> .gro with a properly pre-processed .xtc (-ur -pbc)? Maybe I didn't explain
>> myself properly, but that's what I want to know.
>>
>>
> Yes, if you have removed jumps and have intact structures throughout the
> trajectory, you're fine.  The warning is only there for users who haven't
> thought ahead.
>
> -Justin
>
>
>  /J
>>
>>
>> On Thu, Mar 27, 2014 at 6:32 PM, Justin Lemkul <jalemkul at vt.edu> wrote:
>>
>>
>>>
>>> On 3/27/14, 1:27 PM, João Henriques wrote:
>>>
>>>  Hello everyone,
>>>>
>>>> The documentation reads:
>>>>
>>>> """
>>>> All structures are fitted to the structure in the structure file. When
>>>> this
>>>> is not a run input file periodicity will not be taken into account.
>>>> """
>>>>
>>>> This is rather cryptic, what does it mean in practice? No tpr, no party?
>>>> What if I use a properly centered and whole .gro file?
>>>>
>>>> When ran with a .gro as the structure input file, I get two warnings.
>>>> One
>>>> is related to the masses, which are non-existent in the .gro, but I
>>>> don't
>>>> need them anyway. The second warning is honestly confusing me even more.
>>>>
>>>> """
>>>> WARNING: If there are molecules in the input trajectory file
>>>>            that are broken across periodic boundaries, they
>>>>            cannot be made whole (or treated as whole) without
>>>>            you providing a run input file.
>>>> """
>>>>
>>>> The documentation points out to the structure input file and now it's
>>>> the
>>>> trajectory? What's going on? Do I also need to make each frame whole in
>>>> the
>>>> input .xtc? Can someone elaborate on this?
>>>>
>>>>
>>>>  The documentation consistently refers to the run input file.  A .tpr
>>> has
>>> record of how periodicity is treated.  Nothing else does.  If you don't
>>> tell g_covar (like most Gromacs tools) how periodicity is treated, you
>>> can
>>> get garbage as a result.  The trajectory may have "broken" molecules,
>>> because mdrun doesn't care how they look - it has a run input file and
>>> thus
>>> knowledge of periodicity.  When running analysis like g_covar, if the
>>> bonded connectivity of the molecule and the periodicity are unknown
>>> (again,
>>> if you're not using a .tpr), then absolute displacements of coordinates
>>> are
>>> used, thus your analysis might be totally hosed if the molecule "splits"
>>> -
>>> that would be a rather dramatic structure change detected by g_covar.  In
>>> fact, so dramatic that it's false.
>>>
>>> -Justin
>>>
>>> --
>>> ==================================================
>>>
>>> Justin A. Lemkul, Ph.D.
>>> Ruth L. Kirschstein NRSA Postdoctoral Fellow
>>>
>>> Department of Pharmaceutical Sciences
>>> School of Pharmacy
>>> Health Sciences Facility II, Room 601
>>> 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 601
> 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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> Gromacs Users mailing list
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