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Hi jewettaij,
Recently I am using moltemplate to generate .data file. My system is composed of polymeric anions and Li-ion. So I build the .lt file by dividing the polymer into three parts, i.e. he…
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Longer-term, we probably want to implement the ability to handle non-three-point water models. This will take some substantial work, since amber.build_mixture_prmtop and packmol.pack_box work typicall…
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I am trying to use Packmol 20.14.0 to pack molecules using restart files but I am struggling with the following error:
----------------------------------------------------------------------------…
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First thank you for Packmol! Such a great software.
I've been running into an issue using v 20.15.1 On the a previously working pdb I now have an error
"Reading coordinate file: GLC.pdb
ERROR: …
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Is it necessary to [install the graphics libraries](https://github.com/pak100/Lammps-Tutorial/commit/9b2b43b911c5a5a29c64b4b2c32a24cab4ec2682#diff-bc59f36e2e4e7008e3373c8627ec3ce4R9)? I skipped this s…
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> I can add checks similar to what OpenMM lays out [here](http://docs.openmm.org/latest/userguide/theory/05_other_features.html#periodic-boundary-conditions) if desired
I think that would be a very…
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### Comment:
This is an idea that's been mentioned a few times - with some effort, AmberTools could be released in bits vs. a single monolith that causes conflicts with other packages in users' envir…
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Hi Nil,
Thank u so much for this repo, this had help me put things into perspective.
I notice that u have shared leap.in file for the lipid-only system and not for the protein-lipid system.
…
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Related to #247 - currently Yank has systembuilder, which probably ought to be split off into a more general-purpose tool that will be useful aside from just for Yank workflows (i.e. setup of GROMACS …
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Hi. I use JAX-MD to build a neighbor list, and find some particles that have no neighbors:
(we have 2988 particles in PDB file)
```
DeviceArray([2988, 2988, 2988, 2988, 2988, 2988, 2988, 2988, 2988…