From: Vermaas, Joshua (
Date: Tue Dec 20 2016 - 16:43:39 CST


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. On linux systems that install things to the default directories, you'll find the plugin source files under /usr/local/lib/vmd/plugins/noarch/tcl/qwikmd1.1, and a quick "grep proc *tcl" will show you that you have alot of reading to do so you understand what QwikMD is doing under the hood and what it needs/wants.

-Josh Vermaas

On 12/20/2016 03:18 PM, Danny Xu wrote:

I have hundreds of PDB files that I need to set up for explicit solvement MD simulations. Is there any way to automate QwikMD, process these PDB files and prepare NAMD input files in batch mode?