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Hello,
Is it possible to force an oxDNA simulation to terminate early when a condition is reached? For instance, when a specific base pair is broken, or when the distance between two nucleotides ex…
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**What is the documentation missing?**
The missing information relates to MD simulations on GPU. In the documentation of oxDNA (as of 09.09.2024), the setting "cells_auto_optimisation = false" is pro…
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Ranked by time/complexity:
1. Batch script for running lots of APSIM simulations
2. Combining multiple SQLite databases into one
3. How to create large number of config files? (unsure on how to t…
JBris updated
3 weeks ago
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GROMACS version: 2024.2
GROMACS modification: No
Hello, I'm currently analyzing a few molecules to cross 1,2-Dioleoyl-sn-Glycero-3-Phosphocholine
(DOPC) bilayer. I tried creating DOPC bilayer us…
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[GROMACS tutorial](http://www.mdtutorials.com/gmx/complex/01_pdb2gmx.html )
[GROMACS in the Cloud: A Global Supercomputer to Speed Up Alchemical Drug Design](https://doi.org/10.1021/acs.jcim.2c0004…
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Hi, I would like to use waterkit to perform explicit water placement with predicted .dx files (from other algorithms) without performing any MD simulations.
Can waterkit do that?
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https://github.com/torchmd/torchmd/blob/78063fb38ec0cff366a7d42361947e62efe8112d/torchmd/wrapper.py#L4C1-L30C59
I am using TorchMD to run molecular dynamics simulations. I have a question regarding t…
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This is a super issue to keep track of typos and grammar mistakes in the `main` branch. Just tick off a box when it's resolved.
- [x] `nomad_simulations.md`: "Assign~~e~~ment" should be "Assignment…
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Hello QUIP package managers,
I'd like to be able to train a GAP potential using a dataset of around 100 atoms and then simulate NVT and NPT ensembles containing a few thousand atoms in a larger cel…
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Is it possible to use the software for the calculation of energy differences between a WT monomer and a mutated monomer, both of them are not a complex, so I cannot define a ligand and receptor. I hav…