From: Huebert, David Nicolas (
Date: Wed Feb 02 2022 - 00:19:31 CST

Dear everyone,

I have quite a bit of data and I am hoping to speed up the analysis of many
individual vmd runs by automating it; however, I have been having a problem
with this (and just to note that this is running on an Ubuntu 20.04LTS I
have and not a server. I created a script which attempts to open vmd using
specific files, and then run 1 script with a condition followed by a second
script. Then exits vmd and changes the names of the 2 output files. Then
it is meant to restart VMD and do this all over again. I have tried using
(pipes | ) and echos, and tried -args with the commands after it and all
other routes I could conceive of to achieve this but in the end what occurs
is that either VMD has errors or most commonly it opens vmd, and then it
appears that it doesn't read the next line and when I manually exit out
then it attempts to execute the following lines. I am not sure how to get
VMD to understand these commands as being for it's command line as all of
these lines work properly when I put them in manually but I cannot get them
to work automatically without constant involvement on my part. I am sorry
if this is a basic issue but I am self taught in Molecular Dynamics and as
such I find that I often find myself jumping in the deep end.

The script lines
vmd start_time-Protein.pdb md-Protein-fit-0000-0025.xtc -dispdev none #
Open VMD with structure and trajectory
source /media/david/ORIGIN/PhD-Ubuntu/Gromacs\ Work/Work\ Files\ and\
Programs/sasa.tcl # track residue SASA
residue 35 # must fill in residue number
source ./H2O-Protein-Script.tcl
mv ./SASA_residue\ 35.dat ./Data-SASA-E-Protein_0000-0025.dat # rename SASA
Glutamate Data File
mv ./Data-H2O.xvg ./Data-H2O- Protein-0000-0025.xvg # rename H2O file

# After this point. the pattern is meant to repeat opening different VMD
sessions with the same sourcing and similar file name changes etc. For
thousands of analyses.

I know I am probably missing out on something minor but I don't understand
why my commands are not being entered through the VMD command line.


Mr. David Nicolas Giuseppe Huebert B.Sc. Ph.D. Candidate
Immunology and Infectious Diseases.
Division of Biomedical Sciences, Faculty of Medicine.
Memorial University of Newfoundland.
Room 5357, Health Sciences Building.
300 Prince Phillip Drive.
St. John's, NL A1B 3V6
Tel: 1-(709)-864-6077