VMD-L Mailing List

From: Manish Gupta (magupta_at_syr.edu)
Date: Fri Aug 18 2017 - 15:02:36 CDT

Thanks a lot Chris. Should I write PDB while running simulation or can I convert my already existing lammps trajectory file to PDB and still use this method?

Manish

________________________________
From: Chris Neale <candrewn_at_gmail.com>
Sent: Friday, August 18, 2017 3:53:11 PM
To: Manish Gupta
Cc: vmd-l_at_ks.uiuc.edu
Subject: 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 <magupta_at_syr.edu<mailto: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