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on (especially low resolution) molecular surfaces there are sometimes holes and stray triangles.
![screenshot 10](https://cloud.githubusercontent.com/assets/272250/17562786/34e20764-5ee1-11e6-94f2-1e…
arose updated
7 years ago
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Hi, I would like to suggest two features. I couldn't find how to calculate the _molecular volume_ and SASA (_solvent-accessible surface area_) for a trajectory. Do you think those would be useful addi…
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[Hou, Tingjun, Junmei Wang, Youyong Li, and Wei Wang. “Assessing the Performance of the Molecular Mechanics/Poisson Boltzmann Surface Area and Molecular Mechanics/Generalized Born Surface Area Methods…
cramg updated
3 years ago
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### Details
The computational system is the Ti metal (001) surface containing 72 atoms, and molecular dynamics simulations were performed on it with a timestep of 500 steps and a frequency of 1 fs. T…
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Hi all,
I detected a potential bug. SES surface (Solvent excluded surface) looks exactly the same as the SAS (solvent accessible surface). Reproducible in http://nglviewer.org/ngl/ molecular surfac…
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Hi,
I'd like to use charge flux model as implemented for AMOEBA in the FF that I am working on.
Is this implemented in OpenMM? That's the impression I got from the paper but I wasn't able to locate …
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I have just read the paper cited at the end, and it convinced me about the potential of monolinks as a source of experimental information regarding surface accessibility. As suggested there, this may …
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### Details
Running molecular dynamics simulations of Ti(0001) surface under NVT ensemble using Abacus software. The total timestep is set to 500 steps, but the simulation unexpectedly terminates aft…
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Dear Editors,
I am Xiyuan Wang, the first author of [wang22d](https://github.com/mlresearch/v198/tree/gh-pages/wang22d), "Graph Neural Network with Local Frame for Molecular Potential Energy Su…
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### Team Name:
Qanything
### Project Description:
The potential energy surface (PES) of a molecular system describes its energy in terms of geometric parameters such as internuclear distanc…