[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" <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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