VMD-L Mailing List

From: Axel Kohlmeyer (akohlmey_at_gmail.com)
Date: Fri Jan 01 2021 - 11:03:26 CST

If a trajectory has a significant center of mass drift, that needs to be
first and foremost corrected in the simulation itself. Temperature is
computed with assuming translational invariance. With a thermostat active
the kinetic energy from the system will transfer to the center of mass
drift and can lead to a frozen system (aka flying ice cube syndrome).

That said, many years ago, I wrote some scripts to track some group of
atoms during a simulation in a way John was alluding to. There are some
special considerations necessary to avoid some nausea inducing side
effects.

https://urldefense.com/v3/__http://www.theochem.ruhr-uni-bochum.de/*legacy.akohlmey/cpmd-vmd/part4.html*chap6_sect2__;fiM!!DZ3fjg!pG15GuKklRawkCMdt2fF6AvD3mckLwU0A44fu3t2S1aL5s9C6rUmZrpDdyuFS2QlWw$ 

--
Dr. Axel Kohlmeyer akohlmey_at_gmail.com https://urldefense.com/v3/__http://goo.gl/1wk0__;!!DZ3fjg!pG15GuKklRawkCMdt2fF6AvD3mckLwU0A44fu3t2S1aL5s9C6rUmZrpDdyvuH0Kp5A$ 
College of Science & Technology, Temple University, Philadelphia PA, USA
International Centre for Theoretical Physics, Trieste, Italy
On Thu, Dec 31, 2020, 16:25 John Stone <johns_at_ks.uiuc.edu> wrote:
> It seems this question never got an answer.
> If you read about the various VMD scripting commands, you can
> have VMD do custom visualization operations as a trajectory is
> animated.  There are examples that draw text on each timestep, but
> you could just as well manipulate the camera.  There's no built-in
> feature for what you're asking for however, which is likely why
> nobody on the mailing list replied to your question.
>
> Best regards,
>   John Stone
>   vmd_at_ks.uiuc.edu
>
> On Fri, Sep 18, 2020 at 03:53:22PM +0200, alberto wrote:
> >    Hi,
> >    when I load my lammpstrj, my trajectory moves out focus. with reset
> view
> >    the structure returns in focus.
> >    Is there the possibility to autofocus the structure iteratively?
> >    regards
> >    Alberto
>
> --
> NIH Center for Macromolecular Modeling and Bioinformatics
> Beckman Institute for Advanced Science and Technology
> University of Illinois, 405 N. Mathews Ave, Urbana, IL 61801
> http://www.ks.uiuc.edu/~johns/           Phone: 217-244-3349
> http://www.ks.uiuc.edu/Research/vmd/
>
>