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Add bonds, angles, dihedrals and impropers
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The REST2 transformer should scale the AMAP potentials along with the dihedrals.
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**Describe the bug**
If the user doesn't specify the dihedral or angle the GOMC cannot build the molecule and will crash
**To Reproduce**
Run any simulation and removed dihedral or angle
**Exp…
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Hello, I hope I can explain this right, but I observed the issue as described in the title. Take ethane as an example. it produces the following coordinates:
```
New internal
(redundant) coordi…
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Excuse me, I have the following question
files(dihedral_bend.cpp):
error: expression cannot be used as a function
391 | force->bounds(arg[0],atom->ndihedraltypes,ilo,ihi);
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A one-sided constrain will be very useful during TS conformation search where you want to avoid certain bond formation leading to product but don't want to completely freeze the bond so some alternate…
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I load a gromacs top as a gromacs structure.
Then I add some dihedral and dihedral types to the structure.
When I save that structure as a new gromacs top.
The I-4 pairs will not generate automatic…
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Force field conformer jobs of prenol, 2,3-dimethylbut-2-ene and their radicals, RO2, RO2H, OOQOOH indicates they could possess free CH3 rotors in MMFF94s. Here, I provide an example of prenol.
2D str…
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Dear developer,
I am using the OPLS-AA parameters from the file oplsaa.lt. May I ask for the improper dihedral X_X_003_004, which one should be the center atom?
![image](https://user-images.git…
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I have a test case of heptane and when I set the setting to
```
[scan]
frag_threshold = 1
```
Technically, I would only need to scan two dihedrals. However, I got three dihedrals to scan.
…