[gmx-users] query on plotting dynamical quantity

[Tsjerk Wassenaar]

Hi Jagannath,

You can convert the trajectory to a single PDB file with multiple models.

Cheers,

Tsjerk
On Mar 12, 2016 07:25, "jagannath mondal" <jm3745 at columbia.edu> wrote:

> Hi Tsjerk
>   Thanks for your suggestion on putting the parameters in bfactor column of
> pdb. However, for this, the file format has to be a pdb format. However, if
> I have a trajectory ( in xtc format) and each frame's 'bfactor' values are
> getting updated, then do I need to convert entire xtc files into pdb files
> for visualization?
> Jagannath
>
>
> On Tue, Mar 8, 2016 at 12:43 PM, Tsjerk Wassenaar <tsjerkw at gmail.com>
> wrote:
>
> > Hi Jagannath,
> >
> > Convert the file to PDB format and write the values to the b-factor
> field.
> > Most visualization programs can color by b-value.
> >
> > Cheers,
> >
> > Tsjerk
> > On Mar 8, 2016 06:50, "Jagannath Mondal" <jmondal.backup at gmail.com>
> wrote:
> >
> > > Dear gromacs-users
> > >
> > >   I am sorry to write you a visualization-related query. I hope you can
> > > help.
> > >
> > > My query is: How can I visualize a trajectory file ( example in vmd)
> > where
> > > I have an extra 4th column ( apart from x y z which are first 3
> columns)
> > > which has a dynamically changing variable for each particles ? The plan
> > is
> > > to color gradient the atoms using the values of   4th column.
> > >
> > >
> > > Is there a way to do it. I am sorry again to write you off the list.
> > >  Here is an excerpt from first few lines:
> > > Jagannath
> > >
> > >    219GLN  C  18        6.961000 4.468000 3.776000        1.678980
> > >
> > > 220LEU  C  37        6.753000 4.257000 3.980000          6.526284
> > >
> > > 221THR  C  51        6.618000 4.023000 4.151000          11.323132
> > >
> > > 222ALA  C  61        6.565000 3.742000 4.306000          26.957896
> > >
> > > 223ALA  C  71        6.409000 3.464000 4.313000          52.708403
> > >
> > > 224GLN  C  88        6.213000 3.540000 4.528000
> > > --
> > > 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.
>