Hello Everyone,
I’m new to GROMACS. I want to perform gradual heating/cooling of my system having only water and then eventually moving to complex systems. I would like to know if there is any protocol that I need to adhere to.
Thanks in advance.
Hi Samvidha,
Just some pointers, others in the forum might have more concrete experiences with simulated annealing protocols.
As a method to find the global energy minima, the optimal simulated annealing protocol depends a lot on what system you are looking at - basic parts of the considerations would be: what energy barriers to overcome, how far you want to move from an initial structure, and how stable your model of the system (aka force-field) is with respect to deviations far from the input structure.
If you’re looking at proteins, it’s useful to heat them up just enough that you “melt” some secondary structure, but not so much that you completely disintegrate them. If you want to simulate compound mixtures of simple molecules you might want to go higher in temperature. Notice that also the speed of cooling down can matter, as cooling down very slowly might keep your system trapped in a higher energy state.
For a recent paper that goes into the depth of setting optimal simulated annealing parameters, have a look here:
https://aip.scitation.org/doi/10.1063/5.0018725
You would not be able to use the full adaptive methodology in GROMACS right away, but I found it had useful information on how to think about simulated annealing protocols.
here is some obligatory pointers to the GROMACS documentation: