issues Search Results · repo:RedesignScience/cvpack language:Python

Filter by

• • Code... (...)results
  • Issues8 (8)results
  • Pull requests97 (97)results
  • Discussions1 (1)results
  • Commits0 (0)results
  • Packages0 (0)results
  • Wikis0 (0)results

• State

  • Open
  • Closed

• Advanced

  • Owner
  • State
  • Close reason
  • Has linked pull request
  • Author
  • Assignee
  • Mentioned user
  • Mentioned team
  • Commenter
  • Involved user
  • Label
  • Milestone
  • Number of comments
  • Number of interactions
• Advanced search

Issues8 (8)

8 results

 (69 ms)

8 results

inRedesignScience/cvpack (press backspace or delete to remove)

Sort by: Best match

Filter

RedesignScience/cvpack

Metadynamics NumPy ValueError

I m running a 2D Metadynamics simulation using OpenMM and CVPack (0.12.2) with two collective variables: 1. The z-coordinate of the center of mass of a small molecule 2. The radius of gyration of the ...

• allisonbarkdull
·
• Opened 
  on Apr 23
·
• #106

RedesignScience/cvpack

Getting a `CustomCentroidBondForce` error when attempting to add `RadiusOfGyrationSq` to system.

I m seeing an error when I attempt to implement RadiusOfGyrationSq # Add custom CV for radius of gyration num_atoms = system.getNumParticles() print(f Number of atoms in system: {num_atoms} ) rgsq = cvpack.RadiusOfGyrationSq(list(range(num_atoms)),pbc=False ...

• dsclassen
·
• Opened 
  on Apr 3
·
• #105

RedesignScience/cvpack

Wrong type hint in MetaCollectiveVariable

https://github.com/RedesignScience/cvpack/blob/495518e81b67c578a05e55f9a9166c90589c1472/cvpack/meta_collective_variable.py#L117 The type hint should be Iterable[CollectiveVariable].

• craabreu
·
• Opened 
  on Oct 16, 2024
·
• #104

RedesignScience/cvpack

allowReinitialization flag not used

it looks like whether the flag is set or not the context will always reinitialize? https://github.com/RedesignScience/cvpack/blob/495518e81b67c578a05e55f9a9166c90589c1472/cvpack/utils.py#L141C1-L142C1 ...

• ndnng
·
• Opened 
  on Oct 15, 2024
·
• #103

RedesignScience/cvpack

Coordination CV for centre of mass as an atom

I want to use coordination CV around the center of mass of a group. Is it possible to replace g1 in the Number of Contacts CV with the center of mass of g1? With regards, Sameer

• sameersaurav
·
• 2
·
• Opened 
  on Aug 13, 2024
·
• #102

RedesignScience/cvpack

Question about path CV

Hi, I have been using path CV extensively with OpenMM-PLUMED, and got very excited to learn about your fantastic CV library that runs on the GPU. My understanding, though, is that your path CV defines ...

enhancement

• gitkol
·
• 5
·
• Opened 
  on Apr 16, 2024
·
• #92

RedesignScience/cvpack

A Bug in HelixRMSDContent

Hi, I found a bug in HelixRMSDContent. If I turn on the normalization (normalize=True), it would throw the following error: Traceback (most recent call last): File /home/jyzha/project/enhanced_sampling/test/test_alpha_cv_on_kras4b/run.py ...

bug

• JinyinZha
·
• 1
·
• Opened 
  on Mar 22, 2024
·
• #73

RedesignScience/cvpack

RadiusOfGyration cannot work properly if weighByMass is True

Hi, So I use the following code to define Rg # set umbrella bias n_atoms = top.getNumAtoms() rg = cvpack.RadiusOfGyration(list(range(n_atoms)), pbc=protein.use_pbc, weighByMass=True) rg_bias = mm.CustomCVForce(f ...

bug

• smliu1997
·
• 1
·
• Opened 
  on Aug 28, 2023
·
• #30

Learn how you can use GitHub Issues to plan and track your work.

Save views for sprints, backlogs, teams, or releases. Rank, sort, and filter issues to suit the occasion. The possibilities are endless.Learn more about GitHub Issues

ProTip! 

Press the

/

key to activate the search input again and adjust your query.

Learn how you can use GitHub Issues to plan and track your work.

Save views for sprints, backlogs, teams, or releases. Rank, sort, and filter issues to suit the occasion. The possibilities are endless.Learn more about GitHub Issues

ProTip! 

Restrict your search to the title by using the in:title qualifier.