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

[Mark Abraham]

Hi,

You have a periodic cell, so in general the distance from A to the nearest
periodic image of B is across a cell boundary. Trjconv cannot produce a
trajectory so that all pairs of A and B will have a non-periodic distance
that is the minimum distance. Use a tool that already understands this,
like
http://manual.gromacs.org/documentation/current/onlinehelp/gmx-distance.html
or
http://manual.gromacs.org/documentation/current/onlinehelp/gmx-mindist.html.

Mark

On Mon, Jun 4, 2018, 14:01 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.
> 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
> <
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> >
> 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
> >
> --
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