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Dear,
I'm trying get FRCMOD file from TOP file (Amber). However, I'm getting this message "Unequal dihedral types defined between...". But, when I use "checkValidity" command, I get "...parm7 looks O…
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If a `parmed.Structure` has multiple dihedral potentials for a single set of atoms, then this information is lost in the conversion to the `gmso.Topology`.
I have put together a [gist](https://gis…
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In `_get_dihedral_types` in `lammpsdata.py`, the weighting factor for CHARMM dihedrals is determined as the reciprocal of the length of the list of dihedral terms for a given dihedral. This is probab…
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Hello Selim,
I hope everything's well!
I've been addressing the issue with the spiky MM PES we previously discussed, I eventually ended up adding the ABF scan feature we discussed about in QForc…
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**Tool:**
Glycam structure Evaluation.
**Bug Description:**
Running the structure
```
DGalpb1-4[LFucpa1-3]DGlcpNAcb1-3DGalpb1-4DGlcpNAcb1-2DManpa1-6[DKDNpa2-6DGalpb1-4DGlcpNAcb1-2DManpa1-3]DMa…
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According to http://lammps.sandia.gov/doc/dihedral_multi_harmonic.html the LAMMPS dihedral_style multi/harmonic has only 5 coefficients. However, the conversion of this dihedral from a LAMMPS data fil…
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This XYZ input:
```
17
Cu 0.000000000 0.000000000 0.000000000
N 2.050000000 0.000000000 0.000000000
N 0.000000000 2.050000000 0.000000000
N -2.050000000 0.000000000 0.000000000
N 0.0…
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The Voelz lab is currently building MSMs from simulations of non-protein small molecules and peptidomimetics that don't have the usual phi/psi/chi/omega, etc.
It would seem easy enough to add use…
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**Description**
It takes too long to write LAMMPS data file for a medium system size.
I experienced this when I tried to convert a rather big system, with 174200 atoms, 165400 bonds, 296000 angle…