From: Efthymiou, Christos (
Date: Fri Aug 05 2022 - 03:46:56 CDT


I would like to determine the most efficient way to prepare many simulation files using QwikMD. In reading the VMD manual, I read that it is possible to create a log file for all the commands performed in the GUI, so that the file can be edited and executed. However, when I created a logfile and used QwikMD, the log file did not store any of the commands executed in the QwikMD GUI.

I am aware that the .qwikmd file saves all the commands performed in the QwikMD GUI. However, is it possible to load a .qwikmd file to prepare new simulation files?

For example, I used QwikMD, loaded my PDB file, and selected all the parameters for my simulation before saving the .qwikmd file and then clicking Prepare to prepare all the simulation files. If I wanted to create the simulation files for two additional runs with the same settings, how can I use the .qwikmd file to do this?

If I load the .qwikmd file created previously, everything is loaded into the GUI but the Prepare button is greyed out. Therefore, I cannot select a new folder to prepare new simulation files. If I edit the previously created .qwikmd file with Notepad++ to change the folder path to a separate folder and try loading the edited .qwikmd file, I get an error that there is no "run" folder (as the simulation files have not been prepared yet).

Therefore, I do not understand how to utilize the .qwikmd file or the logging capability of VMD to speed up the simulation file preparation process. I will be preparing simulation files for mutations as well, so it would be very helpful to be able to use some form of scripting rather than the GUI each time.

I also hope to automate the analysis process after running a simulation. Rather than needing to calculate the RMSD, RMSF, etc. using the GUI of QwikMD each time, I would like to record the process once in a log file and be able to run it for each simulation.

I appreciate any guidance on solving this issue.