jslim-furame

NetCDF: HDF error

2

When I run "yank_analyze", I got the following error message: OSError: [Errno -101] NetCDF: HDF error: b'OUTPUT/experiments/solvent.nc' What is the origin of this error and how can I resolve this...

Parallel simulation using slurm queue

3

Let us assume that there are three nodes and each node has 8-GPUs. Is it possible to leverage 24 GPUs simultaneously if there are more than 24 lambda points? In...

yank analyze error

3

I did 10 ns GBSA simulation (number of iterations = 10000, 1 iteration = 1ps). The simulation completed successfully. However, yank analyze gives the following error pymbar.utils.ParameterError: Warning: Should have...

Questions about convergence and sampler

7

I installed the latest yank (0.25.2) and tested it using the scripts given in t4-lysozyme example directory. 1) The first question is: When I increase "default_number_of_iterations" from 500 to 2000,...

Bugs in multistateanalyzer.py

1

I installed the latest version (0.25.2) of yank, but yank analyze does not work properly. This is due to "multistateanalyzer.py". Look at the following lines in "multistateanalyzer.py" (Deltaf_ij, dDeltaf_ij) =...