VMD-L Mailing List

From: Chris Neale (candrewn_at_gmail.com)
Date: Fri Aug 18 2017 - 14:53:11 CDT

Write out PDB files, modify them to have the temperature in the B-value
column, concatenate the PDB files together into a single PDB-formatted
trajectory, visualize in VMD and color by B-value?

On Fri, Aug 18, 2017 at 11:04 AM, Manish Gupta <magupta_at_syr.edu> wrote:

> Hi,
>
>
> I'm running my simulation with LAMMPS. My simulation has varied
> temperature in domain and I want to visualize the simulation based on
> temperature distribution.
>
>
> Since the trajectory file does not contain any information about ensemble
> properties like temperature, I can not get the colors based on it.
>
>
> I think one way of doing it would be to write a reader in Tcl and assign
> the properties to user in VMD, but I'm not sure how to do it. Also, is
> there any other simpler way to get temperature based coloring? I would
> appreciate any help.
>
>
> Thank you
>
>
> Manish
>
>
>