[gmx-users] g_covar warnings

[Justin Lemkul]

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

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