Dear Lammps users
Could anybody introduce me a note or tutorial to learn how to conduct “Umbrella Sampling” in lammps?
This process seems to be easy in GROMACS, however, I could not find proper cases for lammps.
Hi Amir, umbrella sampling is a general free energy calculation technique, which can be applied to a variety of reaction coordinates problems. I presume you refer to the GROMACS tutorial where the two ends of a peptide are pulled: is that what you are trying to do?
If so, a similar approach in LAMMPS uses the Colvars module. If you have carried out the necessary steps to set up and equilibrate a system in LAMMPS, use the example here, which is for a steered MD protocol:
http://colvars.github.io/colvars-refman-lammps/colvars-refman-lammps.html#sec:colvars_crash_course
You will need to adapt the atom selections, of course. Once everything is working for you, you will prepare multiple starting configurations and use a fixed harmonic restraint on each one to run umbrella sampling.
Giacomo
You’re right!
Honestly, I’m seeking an illustrative tutorial to learn umbrella sampling in lammps, similar to that offered by GROMACS.
Thanks for your helpful link.
If there are any other links, please let me know.