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

Dilip.H.N cy16f01.dilip at nitk.edu.in
Tue Jun 5 07:07:50 CEST 2018 

Hi,
I have visualized the molecules in vmd and these two water molecules are
placed diagonally opposite in the box. So, in that case obviously, the
distance will be greater than the box length. And the two water molecules
are within the box only.

And yes, my box here is cubic.

Thank you.



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06/05/18,
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---
With Best Regards,

Dilip.H.N
PhD Student.

On Tue, Jun 5, 2018 at 7:09 AM, Mark Abraham <mark.j.abraham at gmail.com>
wrote:

> Hi,
>
> Only if the box is cubic.
>
> Mark
>
> On Tue, Jun 5, 2018 at 3:20 AM Quyen V. Vu <vuqv.phys at gmail.com> wrote:
>
> > Hi Dillip,
> > As Mark suggest, If you want to calculate by your own code, you can put
> the
> > condition to check which is the nearest neighbour by comparing with box
> > length/2
> >
> >
> > On Mon, Jun 4, 2018, 19:42 Mark Abraham <mark.j.abraham at gmail.com>
> wrote:
> >
> > > 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]
> > > > <
> > > >
> > >
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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=
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> > > > 06/04/18,
> > > > > 5:15:08 PM
> > > > >
> > > > --
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