Noah

How to warm up a system followed by NVT/NPT equilibration while slowly removing backbone constraints

7

Hi, I'm attempting to run some of my first simulations using OpenMM. I want to use the following production pipeline: After applying backbone restraints 1) Energy minimize 2) Slowly warm...

When viewing aligned conformations how to select the best aligned?

2

From the tutorial I have been using the following code block to view the alignment of my prbMol to my refMol. `p = py3Dmol.view(width=400,height=400) dt = {} for i in...

Package versions not included in environment.yml file

3

Trying to install ESPSim locally and conda is taking an age to solve the environment when using the .yml file. It is likely this is due to the .yml file...

Are atomtypes meant to be updated when using repartitionHydrogenMass?

16

Hi, I'm attempting to use HMR with FEP calculations for longer sampling times. I noticed when using the repartitionHydrogenMass method that the hydrogen masses in the [atomtypes] directive of the...

Would it be possible to include an option to apply rot + trans matrix to original PDB as oppose to the cleaned PDB?

1

This would be useful if you are trying to align structures which contain cofactors, such as ligands.

Is reference to bulk water energetics done automatically in CPPTRAJ GIST?

3

Hi, I'm using GIST to measure energetics of water displacement upon ligand binding to a protein cavity. I've been following this [tutorial from ambermd.org](https://ambermd.org/tutorials/advanced/tutorial25/section4.htm). It is my understanding that to...

To undergo GIST analysis can I fit my protein to a reference structure rather than apply strong position restraints?

3

Hi, I've been running MD simulations using OpenMM and want to carry out water analysis using GIST. While I haven't restrained the protein using strong position restraints, as suggested by...

[BUG] BSS.Convert.toRDKit() appears to lose stereochemical information

9

Hey again, I think I've encountered a bug with the Convert module (or I might be overlooking a crucial bit of code). Converting from a BioSimSpace / Sire mol to...

Negatively charged nitrogen parameterisation

2

Hi, I've been encountering an issue with antechamber recently - it seems like it really doesn't like negatively charged nitrogens. [Here is an example molecule in SDF format.](https://drive.google.com/file/d/13zFTDpAJp0rxIQuSG3YQIfB3Zt0tITi_/view?usp=sharing) This is...

Replace calls to jax.tree_[func] with jax.tree_util.tree_[func]

1

As of JAX 0.6.0 (April 16, 2025) [several tree functions have been removed](https://github.com/jax-ml/jax/blob/main/CHANGELOG.md#jax-060-april-16-2025) >From jax: jax.treedef_is_leaf, jax.tree_flatten, jax.tree_map, jax.tree_leaves, jax.tree_structure, jax.tree_transpose, and jax.tree_unflatten. Replacements can be found in {mod}jax.tree or...