Wenhui Shen

How to quickly delete a certain frame in the trajectory

1

Hello Developers: I loaded my **md** trajectory through the following code `traj = md.load('./traj.xtc', top='./ref.gro')` now I want some frames in it to be removed based on some conditions,my current...

Is there a way to remove specific frames from a complete trajectory while keeping the original trajectory intact, without using the join method?

1

Is there a way to remove specific frames from a complete trajectory while keeping the original trajectory intact, without using the join method? The join method is too time-consuming for...

Bayesian Hidden Markov model got an unexpected keyword argument 'desc'

1

When I want to analyze Hidden Markov Network, I have the following problem `hmm=pyemma.msm.bayesian_hidden_markov_model(dtrajs,5, lag=30,stride=10, mincount_connectivity=0.2)` > Sampling HMSMs: 0%| | 0/100 [00:00

How to compute any actual quantity of the coarse-grained kinetics with employing the fuzzy memberships?

7

`bayesian_hmm.gather_stats('transition_model/mfpt', A=[hmm.prior.metastable_sets[1]], B=hmm.prior.metastable_sets[1]).mean` After executing the above code it gives me error: `ValueError: Chosen set contains states that are not included in the active set.` I don't know how to...

Dear MDTraj Developers, I am currently working on a project involving DNA structure analysis, and I have encountered an issue with the mdtraj.kabsch_sander function. Specifically, I am using mdtraj.kabsch_sander to...

Issue with Fast Moving Na Ions in Implicit Solvent Simulation of DNA

3

Dear Developers, I am encountering an issue while simulating DNA with implicit solvent using OpenMM. My system consists of two DNA strands and several Na ions. I have observed that...