VMD-L Mailing List

From: Axel Kohlmeyer (akohlmey_at_gmail.com)
Date: Wed Dec 20 2017 - 10:38:40 CST

On Wed, Dec 20, 2017 at 11:11 AM, Seibold, Steve Allan <stevesei_at_ku.edu>
wrote:

> Hello VMD users
>
> I am simulating a platform structure with a protein on its surface using
> NAMD. I have not fixed the atoms forming the surface platform and so, there
> is rotation after so many ns…I basically would like to remove rotation for
> the movie production…I am attempting to make a movie of the system without
> losing visualization of the protein during rotation.
>
> Is this possible using VMD? or a script pre-written in tcl in VMD?
>
​this is a bit tricky, because you need do do the re-alignment and
re-positioning slowly, or else your movie will be nauseating or might
trigger seizures in sensitive people.

i've worked out some scripting many, many years ago to do this for an ion
pair. this is available in section 6 of the PDF at this link:
https://sites.google.com/site/akohlmey/redirect/cpmd-vmd.pdf?attredirects=0&d=1
mind you, this is very old and thus might need some tweaking to work with
current VMD versions. but then again, VMD has been really good at backward
compatibility of the Tcl scripting interface, so there is a chance, that
adapting this to you system might only need minor adjustments. please note,
that the tutorial in the PDF works incremental, so it may be best to start
reading it from the top and compare to the VMD user's guide on the Tcl
scripting interface while reading.

axel.

>
> Thanks, Steve
> 

-- 
Dr. Axel Kohlmeyer  akohlmey_at_gmail.com  http://goo.gl/1wk0
College of Science & Technology, Temple University, Philadelphia PA, USA
International Centre for Theoretical Physics, Trieste. Italy.