From: João Ribeiro KS (
Date: Tue Dec 20 2016 - 17:19:22 CST


Just to complement what Joshua said.

QwikMD is currently GUI-dependent (for several reasons), making it not so
advisable to automate it through a command line. There are plans to make it
more accessible through command line, but not currently.

However, you can use autopsf, solvate and autoionize within a script to
automate your process. These are the three main plugins that QwikMD uses.

As Joshua pointed out, a blind automation of structure preparation can be
tricky and you may introduce structural errors without noticing.



On Tue, Dec 20, 2016 at 4:43 PM, Vermaas, Joshua <>

> Hi,
> With enough Tcl scripting, anything is possible, but I do need to warn
> you: this seems like an excellent way to make big expensive mistakes by
> making simulation systems that make no sense, so please start small! That
> being said, you can call *any* VMD proc you want from your own Tcl scripts,
> you just need to know where the source code is so you know what the calls
> look like, and expect weird errors if you don't initialize everything you
> need externally, since the GUI-driven procs related to QwikMD or FFTK
> expect text fields to be filled and sometimes refuse to work in text mode--001a1141b10035e8f805441f44b3--