[gmx-users] Re: gmx-users Digest, Vol 111, Issue 53

[Bin Liu]

Hi Trayder,

Thank you for the suggestion. I will try the plugin soon.

Yes, I can play the two trajectories simultaneously, one with protein
disabled. In this way, I indeed can get a very good presentation of what is
happening. However, it's quite inconvenient to set Graphical
Representations in VMD to two trajectories every time. And having two
trajectories to set complicates the Tcl script to automate the
visualization. That's why I ask people how to apply -nojump to a part of a
system.

Cheers

Bin

>
>
> Message: 2
> Date: Thu, 11 Jul 2013 11:51:51 +1000
> From: Trayder Thomas <trayder.thomas at monash.edu>
> Subject: Re: [gmx-users] How to apply trjconv -nojump to a part of a
>         system
> To: Discussion list for GROMACS users <gmx-users at gromacs.org>
> Message-ID:
>         <CAHSz8K7Tc02KXqr6yHQ=c=
> rssocu5gDgxBkrPbk-+-h93ywjdQ at mail.gmail.com>
> Content-Type: text/plain; charset=ISO-8859-1
>
> VMD might do what you want with the PBC tools plugin (installed by
> default). http://www.ks.uiuc.edu/Research/vmd/plugins/pbctools/
> unwrap being the equivalent of -nojump
>
> Otherwise, couldn't you just view your 2 trajectories simultaneously, one
> with protein the other not?
>
> -Trayder
>
>
> On Wed, Jul 10, 2013 at 9:13 AM, Bin Liu <fdusuperstring at gmail.com> wrote:
>
> > Hi All,
> >
> > For the convenience of visualization, I need to remove the jump of one
> > component (say a protein) of the system at the boundary. I don't need to,
> > or say I need not to remove the jump of the other components (say a lipid
> > bilayer), since otherwise the system will look falling apart. I noticed I
> > can cluster a part of a system, then output all the atoms in the system
> in
> > which only the part is clustered, and the other components unchanged.
> Does
> > GROMACS have similar function when *-nojump* is used?
> >
> > If this can not be accomplished directly, is there a way to circumvent
> it?
> > I figured out a way, but haven't implemented it. I can plug the
> coordinates
> > of the protein treated with *-nojump* into the trajectory of the whole
> > system which is not treated with *-nojump*. It is kind of substituting
> the
> > coordinates of one component in one trajectory with the coordinates of
> the
> > same component in another trajectory. Is there anyone aware of a tool or
> a
> > script to do this job?
> >
> > Thank you very much.
> >
> > Regards
> >
> > Bin
> > --
> > gmx-users mailing list    gmx-users at gromacs.org
> > http://lists.gromacs.org/mailman/listinfo/gmx-users
> > * Please search the archive at
> > http://www.gromacs.org/Support/Mailing_Lists/Search before posting!
> > * Please don't post (un)subscribe requests to the list. Use the
> > www interface or send it to gmx-users-request at gromacs.org.
> > * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
> >
>
>
>