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Hello, I will be conducting molecular dynamics for several protein-ligand complexes. Is it possible to calculate the interaction energy between the protein and the ligand for individual simulation ste…
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Greetings,
I'm Marco Ravalli, a phD student working on molecular dynamics by classical interatomic potentials. I'm currently trying to use one of the pretrained MACE models to work with my systems, …
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Connected to #51 #52 #53 #54 - is having our own parsers the best way to move forward? Could MDTraj / MDAnalysis / pytraj / other packages make our lives easier? Note that physical_validation has some…
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Dear team member of bussilab,
I hope this email finds you well. My name is Satyabrata Maiti, and I am working on reweighting distance-based observables using your MDRefine package. I feel this MD…
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- At least one member from each software package development community involved in the comparison should participate, e.g. Standard for performance comparisons of biomolecular simulations,
- When pr…
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Defect Description:
The Simulation page of "Familiarization with the fluorescence Instrumentation" experiment of this lab, the name is given as **Familiarization with the fluorescence Instrumentation…
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I am encountering a segmentation fault while running a LAMMPS simulation using MACE. The error occurs in the PairMACE::compute() function. Below are the details and steps to reproduce the issue.
St…
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Purpose: The molecular weight of several molecules should be easily kept in synch. Thus, only one MW is to be defined as numerical value, whereas others are set by a formula. This procedure currently …
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We need two kind of benchmarks:
- regression benchmarks check the speed of a given algorithm;
- comparison benchmark check the speed of a given simulation for comparison with other codes.
Benchma…