[gmx-users] g_covar warnings

[João Henriques]

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.

/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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