[gmx-users] Distance between the atoms greater than Box length
Quyen V. Vu
vuqv.phys at gmail.com
Tue Jun 5 03:20:17 CEST 2018
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
> > >
> > --
> > Gromacs Users mailing list
> >
> > * Please search the archive at
> > http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before
> > posting!
> >
> > * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
> >
> > * For (un)subscribe requests visit
> > https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or
> > send a mail to gmx-users-request at gromacs.org.
> >
> --
> Gromacs Users mailing list
>
> * Please search the archive at
> http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before
> posting!
>
> * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
>
> * For (un)subscribe requests visit
> https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or
> send a mail to gmx-users-request at gromacs.org.
>
More information about the gromacs.org_gmx-users
mailing list