HanatoK

@bhavranek I think it is simply that the protein-protein calculation is not implemented. Unlike the protein-ligand case, one needs to restrain the fluctuations of side chains of both proteins, and...

I came across the KDL documentation language while using Zellij: https://github.com/kdl-org/kdl At my first glance it is almost compatible with the format that Colvars currently uses, except that strings need...

@giacomofiorin I am not sure about the GROMACS and LAMMPS cases. I use NAMD most of the time, but it doesn't support python officially. As a result, when I want...

I remember Joao has come up some initial python support for NAMD (see https://gitlab.com/tcbgUIUC/namd/-/merge_requests/33), but the PR is still open, and I don't known when it will be merged. My...

> Hi, Thanks for your interest! You may find the file here: https://drive.google.com/file/d/1stCYe3ZGg3GnOrbVqCX_pu2uQ6Frxx6x/view?usp=sharing. Let me know if you have any questions. Thanks for your reply! I downloaded the file but...

@weiHelloWorld Now the script complains about missing `1l2y.pdb`: ``` Traceback (most recent call last): File "./main_work.py", line 1, in from ANN_simulation import * File "/home/yjcoshc/HDD/software/accelerated_sampling_with_autoencoder/MD_simulation_on_alanine_dipeptide/current_work/src/ANN_simulation.py", line 1, in from config...

Thanks @jhenin and @giacomofiorin ! I will try the optimizations if I have time.

@giacomofiorin Is it also possible to parallelize the loops over atoms? I am not familiar with the SMP but it seems it only parallelizes the computation of CVCs and biases,...

@giacomofiorin I will try to make some of the tests MD-engine agnostic. Regarding the threading, is it possible to use a thread pool? I think it might be possible to...

Hi @giacomofiorin! It seems there is no change to the SMP related code, but maybe I miss somethign. If a cvc reuses other ones, how does the SMP work?