hima111997
hima111997
I want to build PLUMED 2.8 for HPC cluster. is it possible and how? Thanks
### Bug summary i ran a NAMD simulation and converted the files to GROMACS to be able to use gmx_MMPBSA and started the calculation with &gb and QH entropy, however,...
i have a protein with some of the coordinates looks like this: ATOM 5063 CG LYS B 316 157.454-100.044 -4.756 0.0187 1.9080 as you notice the X and Y coordinates...
Greeting sir, Thank you for this work. How can I use this model for prediction? Thanks
i am following the tutorial on the pyEMMA website on my system and when i calculate the fraction of used states and counts they appear as 0.38 and 0.48, respectively....
in notebook 07, this line : `hmm_4 = pyemma.msm.bayesian_hidden_markov_model(cluster.dtrajs, nstates=4, lag=1, dt_traj='1 ps', nsamples=50) ` produces this error: ``` --------------------------------------------------------------------------- TypeError Traceback (most recent call last) Cell In[5], line 1...
i have 21 metastable states and when trying to use pyemma.plots.plot_cktest the subplots are very small and i cant see anything. Is there a way to increase the size of...
Is it possible to use pyemma.msm.its on the dtrajs after using TICA on the features? ``` def sample_k_centers_after_tica(n, data): cl_original = pyemma.coordinates.cluster_kmeans(data= data, k=n, stride=1, max_iter=40) its = pyemma.msm.its(cl_original.dtrajs, lags=[1,...
Here's a quick checklist in what to include: when i use add_sidechain_torsions it produces an error: ``` TypeError Traceback (most recent call last) Cell In[62], line 8 5 xtc =...
- [ ] Include a detailed description of the bug or suggestion: i am watching this video https://youtu.be/zvgYjfQ9Vb8?list=PLych0HcnzSQIBl_AZN5L2cMZvOfyhzjd8&t=469 and trying to apply the code on my trajectory. in the part...