giadefa
commented
7 years ago Joao, maybe this deserves a tutorial? I have something for visualizing 2d reaction coordinates
On 4 January 2017 at 12:15, GlebNovikov notifications@github.com wrote:
Dear HTMD users!
I am interesting to test various dimensionality reduction methods, as the alternative to PCA, for my set of MD trajectories of GPCR systems. I would like to cluster all trajectories onto the 2D plane of shared collective variables (meaning that it was calculated from all ensemble of md snapshots) to i) make visualisation of the collective deformations responsible for some biological activity of the GPCR observed in MD; ii) to monitor how the dynamical equilibrium is shifted along those CV in each of the system separately (e.g depending on the presence of various ligands in each case), thus obtaining slice of free energy surface for my systems along CVs or just to make projections of each trajectories separately.
Methodologically, I have prepared my MD data in the manner how I do it for PCA: In brief, I have md three trajectories in dcd format, each consisted of same number of atoms and equal number of snapshots, meaning that share same duration, consisting of only receptors atoms in each case (without ligand, solvent membrane etc) + the pdb of GPCRs with the same number of atoms.
Now in TICA tutorial I don't understand clearly how to load all of those dcd trajectories, fit it to the reference pdb and properly select CVs for the clustering (it's better to make some visualization of it in VMD or another software).
I would be especially thankful for any help or some template script suitable for my task!
Gleb
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GlebNovikov
j3mdamas
gph82
stefdoerr
Dear HTMD users!
I am interesting to test various dimensionality reduction methods, as the alternative to PCA, for my set of MD trajectories of GPCR systems. I would like to cluster all trajectories onto the 2D plane of shared collective variables (meaning that it was calculated from all ensemble of md snapshots) to i) make visualisation of the collective deformations responsible for some biological activity of the GPCR observed in MD; ii) to monitor how the dynamical equilibrium is shifted along those CV in each of the system separately (e.g depending on the presence of various ligands in each case), thus obtaining slice of free energy surface for my systems along CVs or just to make projections of each trajectories separately.
Methodologically, I have prepared my MD data in the manner how I do it for PCA: In brief, I have md three trajectories in dcd format, each consisted of same number of atoms and equal number of snapshots, meaning that share same duration, consisting of only receptors atoms in each case (without ligand, solvent membrane etc) + the pdb of GPCRs with the same number of atoms.
Now in TICA tutorial I don't understand clearly how to load all of those dcd trajectories, fit it to the reference pdb and properly select CVs for the clustering (it's better to make some visualization of it in VMD or another software).
I would be especially thankful for any help or some template script suitable for my task!
Gleb