[gmx-users] obtaining .gro timeframe

[Justin Lemkul]

On 7/1/14, 11:28 PM, Chetan Mahajan wrote:
> Thanks, Justin. *Until now, I was thinking that xtc coordinates are
> wrapped. It's good to know that coordinates from xtc files are unwrapped
> (please comment if not correct, since we talked only with respect to gro

That is correct.  mdrun doesn't care about our visualization convenience.  No 
sense in wasting performance doing imaging on the fly when it's not necessary.

> file). *But I am confused at another thing. I have known at the origin of
> the box is at one of its vertices ( is that not true?). *Then why are some
> coordinates in .gro file (the one generated at the end of gromacs MD run)
> negative, if coordinates are wrapped in the box?*
>

Molecules are made whole; sometimes they're translated in the positive 
direction, sometimes in the negative direction, depending on how the molecule is 
being reconstructed.

> Is my original command using trjconv okay?
>

"OK" is relative.  In this case, you seem troubled by the slight difference in 
convention, but there's nothing "wrong" with the command.  If you want trjconv 
to make molecules whole, use -pbc mol or -pbc whole.  Your original command 
simply dumps the coordinates and does nothing about periodicity.

> Whereas I do get a sample x-coordinate in .gro file, generated at the end
> of MD run (let's call it gro1) from that in .gro file, generated using
> trjconv on xtc (let's call it gro2) by adding a box length to concerned
> coordinate in gro2, (as shown in excerpt 1) , it's only by subtracting a
> boxlength that we interconvert between similar values, as shown in excerpt
> 2 of the SAME file. *Why is there no consistency of conversion between SAME
> two .gro files for all the coordinates? How do I mathematically obtain file
> 2 from file 1 with some consistent measure?  *
>

See above.  trjconv will do it for you.

-Justin

> - : for .gro file at the end of gromacs MD run (gro1)
> + : for .gro timeframe file obtained from .xtc trajectory ( using trjconv)
> (gro2)
>
> *EXCERT 1*
>
> -   11SOL    HW1 2188   3.244   3.071  10.934
> -   11SOL    HW2 2189   3.211   2.940  10.842
> +   11SOL    HW1 2188   0.023   3.071  10.934
> +   11SOL    HW2 2189  -0.011   2.940  10.842
>
>
> *EXCERT 2*
> -   56SOL    HW1 2323  -0.031   1.076   1.130
> -   56SOL    HW2 2324  -0.040   1.096   1.292
> +   56SOL    HW1 2323   3.191   1.076   1.130
> +   56SOL    HW2 2324   3.182   1.096   1.292
>
> Thanks
> Chetan
>
> On Tue, Jul 1, 2014 at 8:10 PM, Justin Lemkul <jalemkul at vt.edu> wrote:
>
>>
>>
>> On 7/1/14, 9:08 PM, Chetan Mahajan wrote:
>>
>>> Thanks, Justin. Are you saying, the coordinates in .gro  file extracted
>>> from xtc trajectory are not wrapped, whereas those in the .gro file
>>> generated at the end of gromacs MD run are wrapped in the box?
>>>
>>>
>> Yes, unless you've manipulated the trajectory in some way with trjconv
>> beforehand.
>>
>>
>>   Now I have a question:  the negative coordinates that are present in the
>>> following text are from .gro file (generated at the end of MD run),
>>> whereas
>>> positive ones are from .gro file obtained using trjconv on xtc.
>>>
>>>
>> Either way, it's a periodicity effect.  Molecules are made whole.
>>
>>
>> -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

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