VMD-L Mailing List

From: Mayne, Christopher G (cmayne2_at_illinois.edu)
Date: Wed Mar 25 2015 - 23:38:03 CDT

Amira,

While we support running some portions in VMD text mode for batch-like runs (as you noted), we don't currently have an an out-of-the-box setup for pipelining. We have some good reasons for this, not the least of which is that the parameterization still requires careful analysis and adjustments to get good results. That said, the entire program is written in Tcl/Tk, which means that if you're willing to dig through the code, it's possible to script every step.

Regards,
Christopher Mayne

On Mar 25, 2015, at 10:09 PM, Amira Yu wrote:

> Hi all,
>
> I'm trying to run a large number of parameterization processes using
> FFTK, with different input files, parameters, etc. for each run. Is
> there a way to do so? It would be very repetitive and time-consuming
> to set the input files and parameters by hand with a mouse for each
> run.
>
> I see that in for example the "Opt. Torsions" tab, there's "Build run
> script" that generate a tcl program, I can then write a program to
> modify this tcl file, and run it in VMD's text mode or the tcl
> console. But in for example "Opt. Geometry" tab, there's no such
> functionality. Is there a way to do this for all the fftk features in
> general? I've tried to use "Log tcl commands to file" but with no
> luck.
>
> Thanks
>
> --
> YU "Amira" Yue
>