Dear all,
I would like to run simulated tempering in Gromacs, but I just found few tutorials or documentation on this subject. From an old thread ([gmx-users] Simulated Tempering in Gromacs 5), it seems that there are some bugs in Gromacs for running simulated tempering. I’m just wondering whether the bug has been solved or not? Thanks!
Dear @obZehn , thank you so much for your reply. I also found a recent thread posted in 2020: [gmx-users] Lambda Weights from Expanded Ensemble Code. Not sure about the current status of this issue.
BTW, would you mind sharing your mdp options for setting up simulated tempering, including the part for setting up the weights? Since I didn’t find any tutorials on simulated tempering in Gromacs, I would greatly appreciate it if you could share your setup. Thank you very much!
Dear @xzeng,
Sorry, my mistake, I answered thinking about simulated annealing, which is different (and much simpler to set up!). I am sorry I am not able to help you in this case. I hope some of the people around here can come and share their mdp files!
Dear @obZehn, thank you for your clarification. Now I’m able to run simulated tempering using the mdvv integrator and c-rescale for pressure coupling. However, mdvv is much slower than md.
A followup here, now I’m able to run simulated tempering in Gromacs. From our short simulations (30ns so far), it seems to be working quite well. Here is also a reference paper which is super useful for setting the initial weights: Phys. Rev. E 76, 016703 (2007) - Choosing weights for simulated tempering
Perfect, thanks for sharing so that there is a reference in the forum as well.
A note here, NVT should be used instead of NPT as higher temperatures will cause the expansion of the simulation box.