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Acellera / htmd

HTMD: Programming Environment for Molecular Discovery
https://software.acellera.com/docs/latest/htmd/index.html
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Question about the version 2.0.3 —— the newTrajectoriesMSM function #1025

Closed jeromeRlon closed 2 years ago

jeromeRlon commented 2 years ago

Hi! I am trying to generate a new synthetic (fake) trajectories sampled from the Markov State Model, it seems like a new function in version 2.0.3. The API from https://software.acellera.com/docs/latest/htmd has not been updated. I want to figure out the meaning of the arguments in the function: newTrajectoriesMSM(self, simlen, ntraj, startFrames=None) and for example, how could i generate a trajectory from a model data from the htmd.model module.

Furthermore, how could i generate a .xtc file from the trajectory of newTrajectoriesMSM?

Thank you so much!!!

stefdoerr commented 2 years ago

simlen is the length of your synthetic trajectory counted in frames. frames times the lagtime of your model will be the total simulation time produced ntraj is the number of synthetic trajectories you want to create startFrames is the frame you want to start the simulation from. It's a bit tricky to use though.

newMetricData() datasource is a MetricData object trajectories are the trajectories produced by newTrajectoriesMSM function

These are very experimental functions though and you might have to experiment with them to get the to work right because I haven't tested them in many years. Ideally first understand what the code does and proceed with caution.

stefdoerr commented 2 years ago

To generate an xtc try this:

newdata = newMetricData(...)
Molecule(newdata.simlist[0]).write("test.xtc")