[gmx-users] Significance of box vectors in GRO trajectory file.

[Dawid das]

By "rewraping coordinates" do you mean how molecules that went outside of
the box are treated?

By the way, why does this vector change during simulation? What if I use
exactly the same vector for my whole
simulation?

Best wishes,
Dawid

2017-06-05 16:08 GMT+02:00 Justin Lemkul <jalemkul at vt.edu>:

>
>
> On 6/5/17 10:07 AM, Dawid das wrote:
>
>> Dear Gromacs Users,
>>
>> Suppose I have a trajectory file in gro format. If I change the last line
>> for each
>> snapshot (i.e. line with box vectors values) into an arbitrary set of
>> three
>> numbers,
>> will it have impact on further manipulations of this gro trajectory file
>> with trjconv?
>>
>> In other words, is the line with box vector significant for a following
>> command:
>>
>> gmx trjconv -f npt-md2-system.gro -o npt-md2-0-0.5ns.gro -s npt-md2.tpr
>> -ndec 6 -pbc mol -center
>>
>> ?
>> I especially worry whether it is going to be fine for -pbc mol and -center
>> options.
>> Do they read this vector at all?
>>
>
> Yes, the box vectors are used for reimaging and if you change them you
> will change both the centering and re-wrapping of coordinates.
>
> -Justin
>
> --
> ==================================================
>
> Justin A. Lemkul, Ph.D.
> Ruth L. Kirschstein NRSA Postdoctoral Fellow
>
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> School of Pharmacy
> Health Sciences Facility II, Room 629
> University of Maryland, Baltimore
> 20 Penn St.
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>
> jalemkul at outerbanks.umaryland.edu | (410) 706-7441
> http://mackerell.umaryland.edu/~jalemkul
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