Re: [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  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"  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  186.961000 4.468000 3.7760001.678980
> >
> > 220LEU  C  376.753000 4.257000 3.98  6.526284
> >
> > 221THR  C  516.618000 4.023000 4.151000  11.323132
> >
> > 222ALA  C  616.565000 3.742000 4.306000  26.957896
> >
> > 223ALA  C  716.409000 3.464000 4.313000  52.708403
> >
> > 224GLN  C  886.213000 3.54 4.528000
> > --
> > Gromacs Users mailing list
> >
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> >
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Re: [gmx-users] query on plotting dynamical quantity

[Tsjerk Wassenaar]

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"  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  186.961000 4.468000 3.7760001.678980
>
> 220LEU  C  376.753000 4.257000 3.98  6.526284
>
> 221THR  C  516.618000 4.023000 4.151000  11.323132
>
> 222ALA  C  616.565000 3.742000 4.306000  26.957896
>
> 223ALA  C  716.409000 3.464000 4.313000  52.708403
>
> 224GLN  C  886.213000 3.54 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-requ...@gromacs.org.
>
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[gmx-users] query on plotting dynamical quantity

[Jagannath Mondal]

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  186.961000 4.468000 3.7760001.678980

220LEU  C  376.753000 4.257000 3.98  6.526284

221THR  C  516.618000 4.023000 4.151000  11.323132

222ALA  C  616.565000 3.742000 4.306000  26.957896

223ALA  C  716.409000 3.464000 4.313000  52.708403

224GLN  C  886.213000 3.54 4.528000
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