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Hello,
I want to use Martini 2.0 with polarizable water model ( doi:10.1371/journal.pcbi.1000810 ) on OpenMM-7.6.0. So, I modfied the relative permittivity to 2.5 in the martini_openmm.py. However,…
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Hi,
I would like to request a feature of using a Merz-Singh-Kollman (MSK) scheme for the grid setting to reconstruct ESPs and fields data from QCArchive.
For the MSK shell grid points, I'd like …
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Hi,
The timing on the announcement for suppressors on VDW is incorrect by a pretty significant amount of time.
Tested today on Warmane Icecrown.
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We are working on supporting [SLipids FF](http://www.fos.su.se/~sasha/SLipids/) with Amber FFs.
SLipids FF is optimized to be used with Amber FFs, but it contains some parameters that are features of…
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## Describe the bug
Rowland-Taylor VdW radii assigned to wrong element after fluorine.
## To Reproduce
Steps to reproduce the behavior:
```py
from mendeleev import element
for i in range(1, …
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Reference epic #6804
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This is a naive question - but does Caviar rely on any of the chemical properties of the protein/biomolecule? Or is it just element and coordinates that are important to the calculation? I would be in…
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Buenas, señor Jiménez.
Yo intentaba unas simulaciones de "docking" entre proteins y ligands. Ejemplos de "Tutorials" (https://lightdock.org/tutorials/0.9.2/index.html) los pude hacer más o menos bi…
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**Describe the bug**
`examples/using_smirnoff_in_amber_or_gromacs/convert_to_amber_gromacs.ipynb` fails when performing an OpenMM System --> AMBER prmtop --> OpenMM System round trip. This happens be…
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Dear martinize2-developer team,
my name is Matthias and I want to use the martinize2 python package to coarse-grain a protein based on the amber ff.
For this purpose, I created two new folders i…