GROMACS version: 2023.3 with CUDA 12.3
GROMACS modification: No
Dear all,
I am doing umbrella sampling based on the Lemkul Lab’s GROMACS Tutorial.
In the tutorial here, there is a script to “iteratively call gmx distance” and on the next page a script contributed by Mike Harms that “extract[s] coordinate files and set[s] up the grompp and mdrun commands to streamline this process.”
Here are the questions I have about the scripts:
- Is the first script applicable to my system if I simply change the com groups?
- Will the second script work as long as I follow the same naming conventions in my sampled configurations, or are there other potential differences in my run I should be aware of?
Here is a screenshot of the second script’s README:
I am also curious as to why “gmx” is left out in the generated .sh scripts for each frame, although the commands edited from the original run-umbrella.sh seem reasonable overall.
Here is a screenshot of run-umbrella.sh in my IDE:
Thank you in advance!