[gmx-users] Distance between the atoms greater than Box length
Mark Abraham
mark.j.abraham at gmail.com
Tue Jun 5 03:40:18 CEST 2018
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]
> > > <
> > >
> >
> 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
> > > >
> > > --
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