From f309a6444bdc2bb18c99d1896be0c035c0d57a38 Mon Sep 17 00:00:00 2001 From: tlfobe Date: Tue, 13 Feb 2024 17:15:59 -0700 Subject: [PATCH] more information about running metadynamics --- README.md | 6 ++++-- 1 file changed, 4 insertions(+), 2 deletions(-) diff --git a/README.md b/README.md index a0d82a5c..bbf401c8 100644 --- a/README.md +++ b/README.md @@ -113,7 +113,7 @@ This command will generate a plain text file, `HBOND_SUMS`, which we can use to Using the "Sum of H-Bonds" timeseries we can estimate good starting parameters for the biased simulations of this system. -### Biased Simulations +#### Biased Simulations Once we have a good initial parameters for the biased simulations we can start running biased metadynamics simulations. Here we take the standard deviation of the unbiased CV and use that as a starting value for the metadynamics hyperparmaeter `SIGMA`. `SIGMA` controls the width of the gaussian biases placed along the CV we are biasing and ultimately determines the resolution of the free energy surface we construct along the CV of interest. Other metadynamics hyperparameters that we need to determine for these simulations are `HEIGHT`, the initial height of the gaussian biasing potentials, `PACE`, the frequency in which biasing potentials are placed, and `BIASFACTOR`, a parameter that controls how quickly biasing potentials decay over time. @@ -184,7 +184,9 @@ $ python signac_project.py run -o submit_all_simulations This will submit 96 simulations to the SLURM scheduler, which can be verified by running `squeue --me`. -#### Bias Exchange Metadynamics +### Multiple Walker Metadynamics Simulations + +### Bias Exchange Metadynamics ## Examples