[gmx-users] obtaining .gro timeframe

[Chetan Mahajan]

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?

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.

Thanks
Chetan


On Tue, Jul 1, 2014 at 7:57 PM, Justin Lemkul <jalemkul at vt.edu> wrote:

>
>
> On 7/1/14, 8:53 PM, Chetan Mahajan wrote:
>
>> Dear All,
>>
>> I need some help to generate .gro file corresponding to a given timeframe
>> of the trajectory obtained in gromacs MD run.
>>
>> Currently, I am using following command to generate a .gro timeframe (5000
>> ps) from .xtc trajectory:
>>
>>
>> *trjconv -f lnanop.xtc -o time5000.gro -s lnanop.tpr -dump 5000*
>>
>>
>> where lnanop.tpr is generated by following command at the beginning of the
>> MD run which geenrates above .xtc file:
>>
>> grompp -f $sethome/prod_lnanopff16.mdp -c $b4prod/lnanop.gro -p
>> $sethome/outff18-2_aftermin.top -o lnanop.tpr -n $sethome/index18-2.ndx
>>
>> where each file means by what is implied by its extension.
>>
>> Now, the comparison of input file to grompp and time0.gro (initial)
>> timeframe generated by "trjconv" command on .xtc looks good. However,
>> there
>> are some differences between the files lnanop.gro (generated at the end of
>> the gromacs MD run) and that generated from "trjconv" command to extract
>> last timeframe of the same xtc trajectory, *although files match on many
>>
>> other accounts. Some of the output of -diff command on two files in the
>> following*:
>>
>>
>> @@ -2322,8 +2322,8 @@
>>      55SOL    HW1 2320   3.174   0.144   7.460
>>      55SOL    HW2 2321   3.041   0.201   7.382
>>      56SOL     OW 2322   0.015   1.114   1.210
>> *-   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*
>>
>>      57SOL     OW 2325   1.398   3.388  10.246
>>      57SOL    HW1 2326   1.471   3.321  10.236
>>      57SOL    HW2 2327   1.365   3.388  10.341
>>
>> - : for .gro file at the end of gromacs MD run
>> + : for .gro timeframe file obtained from .xtc trajectory ( using
>> trjconv):
>> that with no signs, is the common part of the two files
>>
>> What's happening? Please comment. Thanks a lot!
>>
>>
> Periodicity.  The final configuration is "made whole" and atoms are put in
> the box such that they have positive coordinates.  The frames within the
> .xtc file are not whole and not corrected for any particular convention.
>
> -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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