shirtsgroup InterMol issues

shirtsgroup / InterMol

Conversion tool for molecular simulations

MIT License

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issues

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Set coefficients to 0 if they were missing from input file, this is a…

#349 JoshuaSBrown opened 5 years ago
4
Reading Lammps data files (Number of Dihedral Coefficients gives errors)

#348 JoshuaSBrown opened 5 years ago
3
Addressed error with dimension and boundary keywords

#347 JoshuaSBrown closed 5 years ago
1
Bug - in lammps parser caused from using a dict

#346 JoshuaSBrown closed 5 years ago
6
lammps file.data to gromacs files error: intermol.exceptions.UnimplementedSetting: ['pair_style', 'none'] has not yet been implemented in InterMol for LAMMPS.

#345 ananvodo opened 6 years ago
6
Desmond conversion

#344 tjgdamen opened 6 years ago
6
DLPOLY maybe?

#343 sperezconesa opened 6 years ago
1
Possible bug in GMX2LAMMPS energy evaluation with waters.

#342 sperezconesa opened 6 years ago
1
Desmond to GMX

#341 billy-noonan opened 6 years ago
4
Issues with installing InterMol

#340 yinglongmiao opened 6 years ago
19
Removing time bottlenecks for Desmond parsing

#339 mrshirts opened 7 years ago
6
Fix for .gro file output with too many atoms.

#338 mrshirts closed 5 years ago
0
Desmond to gromacs conversion failing to parse quoted string

#337 sup27606 opened 7 years ago
15
sum_parameters?

#336 mrshirts opened 7 years ago
4
constraint fixes + fix for amber boxes

#335 mrshirts closed 7 years ago
0
Updating changes implemented in the freesolv exercise

#334 mrshirts closed 7 years ago
0
Desmond to gromacs

#333 Dileepvijayan opened 7 years ago
2
Amber to Desmond

#332 yiannisgaldadas closed 5 years ago
4
Lammps errors with default parameters

#331 mrshirts opened 7 years ago
0
Conversion from Desmond cms to Gromacs

#330 yingyang90 opened 7 years ago
11
Add an option to specify the output units

#329 maaren opened 7 years ago
2
replaced simtk.unit with parmed.unit

#328 maaren closed 7 years ago
1
Handle comparison of inputs of Amber files without box size

#327 mrshirts opened 7 years ago
0
mismatch in imported module name and name used.

#326 mrshirts closed 7 years ago
0
Use the ParmEd units module, instead of OpenMM

#325 mrshirts closed 7 years ago
1
Only raise error for missing LAMMPS when called

#324 ctk3b closed 7 years ago
12
Have other codes call CHARMM when running unit tests.

#323 mrshirts opened 7 years ago
0
Add CHARMM as an input file for testing.

#322 mrshirts opened 7 years ago
0
Can't specify different binaries for testing

#321 mrshirts opened 7 years ago
0
Address issues raised by Xubo lin with incorrect conversion to desmond

#320 mrshirts closed 7 years ago
2
Ensure that dihedraltype matching exactly matches gromacs logic

#319 ctk3b opened 7 years ago
0
LAMMPS dihedral_style multi/harmonic coefficients mismatch

#318 b-v opened 7 years ago
4
Only complain about lammps binary not found if it is needed.

#317 mrshirts closed 7 years ago
0
newlines in the -ls option are not passed through (#315)

#316 maaren closed 7 years ago
1
newlines in the -ls option are not passed through

#315 maaren closed 7 years ago
2
Pairtypes are missing in the generated lammps input

#314 maaren opened 7 years ago
1
reorder atom_orders starting from best match (#312)

#313 maaren closed 7 years ago
3
InterMol selecting the last match for dihedrals?

#312 mrshirts closed 7 years ago
5
Merging/increasing compatibility with ParmEd

#311 ctk3b opened 7 years ago
2
Multiple entries for same molecule type in [ molecules ] break G->L conversion

#310 ctk3b opened 7 years ago
5
GROMACS dihedraltype lookup appears to choose first successful lookup

#309 ctk3b closed 7 years ago
2
Simplify energy grouping accross simulators

#308 ctk3b closed 7 years ago
18
Correctly group non-bonded energies in output

#307 ctk3b closed 7 years ago
0
Remove upper limit on # atoms in LAMMPS forces

#306 ctk3b closed 7 years ago
0
Print LAMMPS UB angles as float

#305 ctk3b closed 7 years ago
0
[WIP] fix for writing of virtuals in Desmond

#304 mrshirts opened 7 years ago
1
Add missing call to process vsites

#303 ctk3b closed 7 years ago
0
Impement virtual site 2,3,4 parsing in GROMACS

#302 ctk3b closed 7 years ago
1
Fix typo in LAMMPS pair_coeff writing

#301 ctk3b closed 7 years ago
0
.gro writing currently overruns the 5 length field width

#300 mrshirts closed 7 years ago
1

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