[gmx-users] writing trajectory of an atom

[Dallas Warren]

http://manual.gromacs.org/documentation/current/user-guide/mdp-options.html?highlight=mdp#mdp-compressed-x-grps

And specify the particular atom in a group you pass in an index file to
grompp.

Catch ya,

Dr. Dallas Warren
Drug Delivery, Disposition and Dynamics
Monash Institute of Pharmaceutical Sciences, Monash University
381 Royal Parade, Parkville VIC 3052
dallas.warren at monash.edu
---------------------------------
When the only tool you own is a hammer, every problem begins to resemble a
nail.


On Wed, 18 Dec 2019 at 11:20, Hadi Rahmaninejad <ha.rahmaani at gmail.com>
wrote:

> Hi Salman
>
> Thanks, but in this way I will save trajectory of all of the atoms in the
> trr file, and then I extract just the trajectory of my atom. However, what
> I need is to avoid savimg lots of data. I needed an option in my mdp input
> file. Do you have any idea for that?
>
> Thanks
> Hadi
>
> Sent from my iPhone
>
> > On Dec 17, 2019, at 5:37 PM, Salman Zarrini <salman.zarrini at gmail.com>
> wrote:
> >
> > Hi Haid,
> >
> > In your index file, you should first generate a group which contains only
> > the atom of your interest:
> >
> > gmx mak_ndx -f case.gro -o index.ndx
> >> a atom
> >> q
> >
> > Then you can extract the trajectory of that single group (single atom)
> > using:
> >
> > gmx trjconv -f traj.xtc -n index.ndx -o atom.xtc
> >> choose the group of your interest here!
> >
> > Regards,
> > Salman
> >
> > On Tue, Dec 17, 2019 at 4:04 PM Hadi Rahmaninejad <ha.rahmaani at gmail.com
> >
> > wrote:
> >
> >> Hello Dear gromacs users,
> >>
> >> To reduce the size of my xtc file, I need to just extract the
> trajectory of
> >> a especial atom, which is not an independent group, it is just one atom
> in
> >> a group. I know that in md options I can narrow down trajectory of a
> group
> >> (xtc_grps = XXX), but for just one atom or molecule in that group I
> cannon
> >> find. I appreciate if any user can give me some hint,
> >>
> >> Thank you,
> >> Hadi
> >> --
> >> 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.
> --
> 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.
>