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### Library and Version
PhysX v5.4.1
### Operating System
Windows 11
### Steps to Trigger Behavior
1. Download [this sample program](https://github.com/LSBUGPG/PhysXJump)
2. Compile …
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Dear developers,
I am using CP-VASP version 2.0 to run AIMD simulations and have encountered an issue with abnormal fluctuations in OSZICAR. The solvation plugin I am using is VASPsol++. My system co…
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I realized yesterday that `Calc_dt_1D`, `Calc_dt_2D`, and `Calc_dt_3D` all ignore the dual-energy formalism.
It would probably be more correct to use the internal energy in the regime where kinetic…
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Add a simulation for an n-level quantum system.
Requirements:
- Visualization of an analog to an ensemble (Coupled to a heat bath with a specific T?)
- Real-time histogram of populations in diffe…
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It is well-known that preparing the files for molecular dynamic (MD) simulation of protein-ligand complex is a tedious process, which includes preparing ligand topology, solvation, adding ions, energ…
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Some MLFF models expose properties other than the forces and energies. For example, [CHGnet](https://www.nature.com/articles/s42256-023-00716-3) also predicts the magnitude of the magnetic moment. Is …
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### **Feature Request: Create a `Tracker` Class for Monitoring Simulation Metrics**
#### **Description**
We need a flexible `Tracker` class that can be inherited by other classes to track specific…
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This becomes an issue when restarting simulations that have been set up with pyMBE since it breaks the setup of the reaction methods, which cannot be checkpointed with the current funtionalities in ES…
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When performing molecular dynamics (MD) simulation with a PDB file containing Zn2+ ions, the ion representation is lost after the energy minimization step.
Zinc ion part in our input pdb file:
`HE…
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Hello,
I am trying to run a REST2 simulation to fold/unfold small peptide (chignolin and TrpCage).
It seems that `femto` is more adequate to study protein ligand system, but it looks anyway doable…