Umbrella Sampling with Hoomd #2075
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Dear Community, I'd like to run umbrella sampling using hoomd-blue. However, I realize that hoomd doesn't have built-in function for it. The common plugin PLUMED, I believe, is not compatible with Hoomd. I searched online and found there is a pacakge called PySAGES that's capable of doing umbrella sampling with Hoomd but it was only tested till Hoomd.v4. I'd like to ask how to do umbrella sampling with hoomd-blue, specifically, how to apply harmonic potential to the distance between the centers of two groups. I’m comfortable with doing postprocessing myself once the biased simulation data is generated. Thank you in advance for your help! |
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Replies: 2 comments
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I don't maintain PySAGES, so you'll have to ask on their support channels for help if you chose to use that package. Many have used HOOMD-blue for umbrella sampling implemented in Python scripts. The most straightforward way is to evaluate your order parameter in Python and use |
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Dear Dr. Anderson, Thank you for your quick reply. It is of great help and I managed to apply the umbrella samling with your suggestion. Thank you! |
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I don't maintain PySAGES, so you'll have to ask on their support channels for help if you chose to use that package.
Many have used HOOMD-blue for umbrella sampling implemented in Python scripts. The most straightforward way is to evaluate your order parameter in Python and use
get_snapshot / set_snapshotto apply Monte Carlo moves. I don't provide this directly in HOOMD-blue because there are so many different order parameters that people use and there is no one interface that will work for all of them.