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As I know, openmm supports the GROMACS input file such as .gro and .top file.
My question is whether openmm also supports the gromos54a7 united-atom force field formatted GROMACS input file format (.…
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I have encountered an errors when I use quite a long path to my pdb files to build the system with packmol. Please find below the error:
`At line 407 of file output.f90 (unit = 15)
Fortran runtime e…
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Some blocks need special attention and should maybe override the __eq__ methode the inherit from the generic_block
- [x] FORCEFIELD
- [x] MAKETOPVERSION
- [ ] DISTANCERESSPEC
- [ ] MPERTATOM
- …
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With atomistic force fields, usually one uses a line such as the following in the TOP file:
```
#include "gromos53a6.ff/forcefield.itp"
```
which tells GROMACS to look in `/usr/local/gromacsXXXX/s…
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Thank you for creating this repository!
I am working with a united atom trajectory which causes issues at the the `fp.run` method:
```
lig = u.select_atoms("resname LIG")
prot = u.select_atoms…
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`Molecule.to_hill_formula` is actually a staticmethod, taking a `Molecule`, whereas `Molecule.hill_formula` is the property which actually gives a Hill formula. This is sort of ugly compared to all t…
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Thanks for the great package!
Just spotted a typo in the README
`from SMArt.md import parse_top, parse_ff
ff_gr = parse_ff(gromos_ifp_file) # by default, format_type = 'gm'
ff_gm = parse_ff (gro…
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In ``tutorial_gromos_pipeline.ipynb``, cell 16 causes an error:
```
cnf = Cnf(cnf_eq_NVP)
trc = Trc(out_eq_NVP+".trc")
trc.cog_reframe(cnf)
trc.visualize(cnf)
```
The error reads:
```
-…
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In the file https://github.com/gromacs/regressiontests/blob/master/complex/nbnxn-free-energy-vv/reference_d.warn the waring mentions a stale url https://redmine.gromacs.org/issues/2884
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In the TI example notebook `examples/example_TI_gromos_simulation.ipynb`, the file `/examples/example_files/TI_Calculation/TI_input/M030_6KET.disres` is specified, but this file isn't in the repositor…