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Hi, I am interested in using radical.pilot and it seems to work well for my purposes when it comes to running multiple independent Molecular Dynamics (MD) simulations on one node, within one HPC job. …
dz24 updated
18 hours ago
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How do we visually summarize a MSM?
- Naive: draw a network where the nodes are exemplars of each state and edges are transition rates, e.g.
![image](https://cloud.githubusercontent.com/assets/57590…
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When I run the FM1 tutorial example with the following execution:
```
(sire) spadavec@Crandall:~/itx/sire_example/ligandswap$ ligandswap -t0 rec_fmc.top -c0 fmc.30.crd -l0 FM1 -t1 rec_cti.top -c1…
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Describe data for clarity and sharing
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**Describe the bug**
In the output of GFN-FF molecular dynamics for a sphere of 500 water molecules (and other systems) the total energy and the potential energy in xtb.trj file show a nonphysical tr…
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reported by: @CloudyLex
```
Title:
Stark broadening of lines from transition between states n = 3 to n = 2 in neutral helium. An experimental and computer-simulation study
Authors:
Gigosos, M. A.…
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DiffEqJump now has spatial SSAs. Thats awesome.
I was wondering whether modeling interparticle forces between pair of molecules is important in this area of jump processes on spatial grids. (Not v…
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HelloProfessor,
What I am trying to do is separate a small DNA fragment from the binding pocket of a protein and plot the free energy path. Should I use BFEE for this purpose, considering a DNA mole…
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It might be a good idea to add the possibility to run SENPAI with simulation parameters loaded from an external file.
This would for example ease running the same simulation on multiple files in seq…