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I'm trying to create a coarse-grained model for a virus with an atomic model consisting of 60 chains, each having around 500 amino acids. When I use the following command for coarse-graining,
`mar…
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Add a function to cmeutils that takes in a gsd snapshot of an atomistic system and the CG mapping (obtained from grits), and it creates a freud system based on the CG beads. The resulting freud syste…
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As discussed in [Create MolecularSystem class](https://github.com/js850/PyGMIN/issues/49), it would be nice if we could create some sort of topology module for PyGMIN.
So far, we want to be able to i…
khs26 updated
11 years ago
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The purpose of this issue is to suggest building a "component" for auto_martini (dubbed `mmic_ffpa_autom`) that makes it part of the [MMIC](https://mm-portal.netlify.app/mmic) ecosystem [MolSSI](http:…
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Dear developers,
I attempted to calculate coarse-grained partial charges for graphene-like molecules using a Python script.
Initially, my atomistic model comprises ~ 40 atoms and, after coarse…
yel21 updated
2 years ago
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Post questions here for this week's exemplary readings:
3. Klingenstein, Sara, Tim Hitchcock, and Simon Dedeo. 2014. “[The Civilizing Process in London’s Old Bailey](http://www.pnas.org/content/111…
lkcao updated
10 months ago
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Hi, I'm encountering issues related to random field mesh element values being evaluated exclusively at the centroid, where this value isn't representative for larger elements.
I've implemented a so…
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Hi, I am running the opt_example code on a multi-molecule system (liquid) and find the output save_traj output each molecular trajectory in different time steps, instead of combine all molecules in on…
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Fine-graining is not implemented for system sized morphologies. It would be a good proof of concept to show that we can take a UA trajectory, add hydrogens, and run the relaxation workflow Matty descr…
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Hi,
I want to apply your code to simulate the magnetization of a 2D star-hexagon lattice possessing 4 sites in a unit cell.
The system is in the presence of an external magnetic field.
Does your…