GROMACS version: 2020.3
GROMACS modification: Yes/No
Recently, I am try to learn how to use GROMACS. And these .mdp files make me confused. So, I want ask a favor how learn to construct personal .mdp file. Where can I find some suggestions? I read l paper on amber99sb-ind, but I can’t find any hints about how to set these parameters in ,mdp?
Best
xinxinzhu
Hello xinxinzhu,
These tutorials by Justin Lemkul are very helpful and include mdp files with explanations of what each of the parameters does:
http://www.mdtutorials.com/gmx/
The Gromacs manual is also helpful:
https://manual.gromacs.org/documentation/current/user-guide/mdp-options.html
If you run a simulation with a completely blank mdp file (nothing in it), the default options are selected and Gromacs outputs an mdp file (mdout.mdp) that lists which parameters were selected (the default ones in this case).
There is also a Bioexcel webinar that explains some of the options (and there’s a lot of other useful webinars there as well):
All of these resources were helpful for me when I was starting out.