[gmx-users] Distance between the atoms greater than Box length

[Dilip.H.N]

Hello all,
I have extracted the trajectory of my system containing all the water
molecules and my box length is 2.48 ~2.5 nm.
The command was:
gmx trjconv -f nptmd.xtc -s nptmd.tpr -pbc mol -o nptmdtrjwater500.gro -dt
60      #i have 60000 frames (30ns is the time and saved the coordinates
for 0.5 ps )and i have extracted a total of 500 frames trajectory (-dt 60
=>30000/500).

And i have written a code which calculates the inter-atomic distance (in my
case it is inter oxygen distances). And when i calculate it (using the
distance formula ie.,
{sqrt [(x2-x1)**2+(y2-y1)**2+(z2-z1)**2]} the distance between the oxygen
atom of say, 7SOL and 6SOL, the distance comes to 3.4520.

Here are the coordinates for two water coordinates as representative...

Generated by trjconv : Glycine-Water t=   0.00000
xxx
    .
    .
    .
    6SOL     OW   13   2.405   0.185   1.774
    6SOL    HW1   14   2.452   0.097   1.782
    6SOL    HW2   15   2.466   0.259   1.804
    7SOL     OW   16   0.016   2.177   0.277
    7SOL    HW1   17   0.098   2.141   0.234
    7SOL    HW2   18  -0.064   2.126   0.245
    .
    .
    2.49238   2.49238   2.49238

How is this possible ie., 3.452 nm, which is greater than the box length
(2.5 nm). How can the interatomic distance be greater than the box
length..??

Any suggestions are appreciated.

Thank you.

[image: Mailtrack]
<https://mailtrack.io?utm_source=gmail&utm_medium=signature&utm_campaign=signaturevirality5&>
Sender
notified by
Mailtrack
<https://mailtrack.io?utm_source=gmail&utm_medium=signature&utm_campaign=signaturevirality5&>
06/04/18,
5:26:50 PM

---
With Best Regards,

Dilip.H.N
PhD Student.

On Mon, Jun 4, 2018 at 5:15 PM, Dilip.H.N <cy16f01.dilip at nitk.edu.in> wrote:

> Hello all,
> I have extracted the trajectory of my system containing all the water
> molecules and my box length is 2.48 ~2.5 nm.
>
> And i have written a code which calculates the inter-atomic distance (in
> my case it is inter oxygen distances). And when i calculate it (using the
> distance formula ie.,
> {sqrt [(x2-x1)**2+(y2-y1)**2+(z2-z1)**2]} the distance between the oxygen
> of say
> 6SOL     OW   13   2.405   0.185   1.774
>     6SOL    HW1   14   2.452   0.097   1.782
>     6SOL    HW2   15   2.466   0.259   1.804
>     7SOL     OW   16   0.016   2.177   0.277
>     7SOL    HW1   17   0.098   2.141   0.234
>     7SOL    HW2   18  -0.064   2.126   0.245
>
>
> ---
> With Best Regards,
>
> Dilip.H.N
> PhD Student.
> [image: Mailtrack]
> <https://mailtrack.io?utm_source=gmail&utm_medium=signature&utm_campaign=signaturevirality5&> Sender
> notified by
> Mailtrack
> <https://mailtrack.io?utm_source=gmail&utm_medium=signature&utm_campaign=signaturevirality5&> 06/04/18,
> 5:15:08 PM
>