From: Efthymiou, Christos (
Date: Thu Sep 01 2022 - 08:48:31 CDT


I have two questions regarding QwikMD. I use a Windows 10 computer and VMD 1.9.3.

First, is it possible to automate the analysis offered by QwikMD? For example, I would like to have a script that performs RMSD, RMSF, H-Bonds within the solute, between chains, etc. analyses so that I can run the script and generate .dat files for each characteristic rather than having to use the GUI. Is it possible to find the scripts/commands that QwikMD uses to calculate each of these? Ideally, I would like to use the GUI once for a trajectory, recording all the settings I use for each analysis, and then have a script that I can use on other trajectories.

Second, it would be helpful to have such a script as currently I am only able to load the trajectory containing water molecules into QwikMD. I ran simulations using QwikMD/NAMD, but the trajectory is very large and causes VMD to crash. Right now, to be able to use QwikMD, I must set a high stride value to prevent crashing.

I have used catdcd to reduce the size of the MD.dcd trajectory by removing all the water molecules and ions, but this edited trajectory does not show up as an option to load when I load the .qwikmd file. Is it possible to use the QwikMD analysis features with an edited dcd file?

The only potential solution I can think of is to rename the dcd/psf/pdb files I created without water to the names of the solvated versions (thereby requiring me to change those to something else) to "trick" QwikMD into using the edited files. However, I would prefer to not have to go through this process every time I want to analyze my trajectories, so I appreciate any other workarounds to this problem.

Thank you for any advice.