From: Norman Geist (
Date: Mon Aug 21 2017 - 00:08:08 CDT

Just my notes: Since the temperature of single particles fluctuate extensively, you won’t probably see anything else than a rainbow colored molecule, were particles can range from 1000K to 5K, unless you use averages of the temperature, regardless of how you will visualize it in the end. At our site, we use a own tool that computes the temperature in a 3D grid through the simulation cell as a *.dx file and uses VMD’s “Volume Slice” drawing method to visualize it. But usually, the temperature distribution is just fine along the cell, and along atoms of various types.


The only significant thing I’ve ever learned from it, is that one is absolutely forced to use SHAKE (aka rigidbonds) for TIP3P water, otherwise the waters oxygens are too hot and transfer that wrong temperature to the solute too, since the hydrogens don’t have a VDW radius.



Norman Geist


Von: [] Im Auftrag von Chris Neale
Gesendet: Freitag, 18. August 2017 21:53
An: Manish Gupta <>
Betreff: Re: vmd-l: Visualize temperature


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 < <> > wrote:



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