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The current pattern in the toolkit is to populate forces by iterating through `ParameterHandler` objects and calling the `create_force` method of each. For exporting to OpenMM, this requires some cust…
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**使用Zotero向word插入参考文献时,有部分期刊文献的引用格式错误地使用了会议论文的格式**
CSL 样式:418huazhong-university-of-science-and-technology.csl
插入参考文献时,绝大多数文献格式正确,但是个别文献插入的格式错误如下:
[1] X. Qian, J. Zhou, G. Chen. Phonon-engineer…
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I translated `findBlocksWithInteractions` to Metal Shading Language and ran it through Metal Frame Capture ([source code](https://github.com/philipturner/openmm-benchmarks/blob/09d58d0e62c7d981ce9eb64…
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Hello,
I want to use multiple gpus with the ReplicaExchangeSampler and MultiStateReporter to produce trajectories for an HREMD simulation. Although the system appears to get setup properly and the…
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Hi there,
While generating the ligand topology (parameters), I am getting the following error for the RNA-drug complex (6XB7).
Could you please advise on this matter ?
Thank for your help.
…
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The `mda.coordinates.TRJ.NCDFReader` expect an Amber-generated NetCDF trajectory to have `time` information in the `variables` object of the NetCDF file.
This is true for NetCDF files created by AMB…
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Currently, we have 2 sets of van der waals parameters, depending on whether it is an inter- (higher energy) or intra-chain (lower energy) edge. The difference is approx. 10-fold for the epsilon parame…
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:clipboard: **Description**
Could you provide a badge for google scholar?
This badge is used to show how many times a paper is cited.
e.g: "cited by | 283"
![image](https://user-images.githubu…
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Hey,
I have been playing around with the tutorial [notebook](https://mybinder.org/v2/gh/OpenFreeEnergy/ExampleNotebooks/HEAD?labpath=openmm-rbfe%2FOpenFE_showcase_1_RBFE_of_T4lysozyme.ipynb) - but …
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### 9/15 Agenda
1. - [x] reference letter
Genome Biology and Systems Degree Program
2. - [x] progress report, short discussion of the following steps and the schedule from now to version 1
workf…