[gmx-users] obtaining .gro timeframe

[Chetan Mahajan]

Thanks a lot, Justin. It's much clearer, but one last question: If the
coordinates in sample.gro extracted from xtc trajectory using trjconv (
without any application of pbc) are unwrapped, why almost all of them
happen to lie in the box, as can be seen in the following snapshot? I would
expect many of them scattered in space, beyond original box?

https://www.dropbox.com/sh/1za0snsw20is106/AADU7hG_CMQmtZ8iI4XGKz-va

Dark blue line is the box boundary.

Thanks
Chetan


On Wed, Jul 2, 2014 at 5:14 AM, Justin Lemkul <jalemkul at vt.edu> wrote:

>
>
> 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
>>>
>>> ==================================================
>>> --
>>> 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 601
> 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.
>