-
Dear all,
I am trying to perform ANM calculations on a tetrameric membrane protein (PDB ID 3J8H, chains A,C,E,G) using only CA atoms, which amount a total of 14640 atoms. In our unversity we have a c…
-
Hello,
I am seeing this new error when coarse graining a density with create_gmm.py
```
sampling points
fitting gmm
creating GMM with n_components 350 n_iter 100 covar type full
fitting
Tra…
-
Good morrow.
I have been trying to use martinize2 for coarsegraining a protein+lipid+water system, and every single job I have run has been killed prematurely with the added issue that all residues…
-
It looks like `snap.bonds.groups` is being populated correctly, but `bonds.types` and `bonds.typeid` are not when saving the coarse-grained GSD file. This is an issue if you're wanting to use GRiTS t…
-
Hi Tristan,
First of all, I would like to thank you for your program Auto_martini.
My problem is that I'm trying to use this script to coarse grain a small organic molecule: PK11195 (C21H21ClN…
-
In my sumlutions, there are two kinds of peptides, named peptide-A and peptide-B. The number for each peptide is ten, and was solvated in water. So, the simulation box is consisted of ten pieces of pe…
-
Posting the same issue in the torchmd-net repo as it might be a joint issue.
I am trying to train a NNP on chignolin trajectories in explicit solvent with TorchMD-Net, which I then plan to use in O…
-
Posting the same issue in the openmm-torch repo as it might be a joint issue.
I am trying to train a NNP on chignolin trajectories in explicit solvent with TorchMD-Net, which I then plan to use in …
-
@JuliaRegistrator register
-
I'm unable to find documentation on the timescale of the mode vibrations when visualized in VMD NMWhiz. Is there an arbitrary time-scale set when finding the modes and solving the equations of motion?…
jpajs updated
10 months ago