[gmx-users] query on plotting dynamical quantity

[jagannath mondal]

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
> > --
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