SPICA-group/spica-tools: v1.0.0

This release is the first version available for CG-MD simulation setup for SPICA and pSPICA as performed in the following paper:

• SPICA
  • https://pubs.acs.org/doi/10.1021/acs.jctc.8b00987 (lipid model)
  • https://pubs.acs.org/doi/abs/10.1021/acs.jctc.1c01207 (protein model)
  • https://pubs.acs.org/doi/10.1021/acs.jctc.3c01016 (improved protein model)
• pSPICA
  • https://pubs.acs.org/doi/abs/10.1021/acs.jctc.9b00946 (lipid model)
  • https://pubs.acs.org/doi/10.1021/acs.jcim.3c01611 (protein model)

What's Changed

• Mod python3 by @onefive13 in https://github.com/SPICA-group/spica-tools/pull/2
• modified error of setup_lmp.py by @yamatetsu1102 in https://github.com/SPICA-group/spica-tools/pull/3
• Setup gmx by @yamatetsu1102 in https://github.com/SPICA-group/spica-tools/pull/4
• Arrange by @yskmiyazaki in https://github.com/SPICA-group/spica-tools/pull/5
• include ischarged val to sysdat class by @yskmiyazaki in https://github.com/SPICA-group/spica-tools/pull/6
• Go model by @yamatetsu1102 in https://github.com/SPICA-group/spica-tools/pull/7
• modified angle_style by @yamatetsu1102 in https://github.com/SPICA-group/spica-tools/pull/9
• add terminal types for pspica option by @yskmiyazaki in https://github.com/SPICA-group/spica-tools/pull/10
• modify angle for protein by @yamatetsu1102 in https://github.com/SPICA-group/spica-tools/pull/11
• modify output of angle by @yamatetsu1102 in https://github.com/SPICA-group/spica-tools/pull/12
• Change "cmp_wc" function and add small changes for pSPICA by @yskmiyazaki in https://github.com/SPICA-group/spica-tools/pull/13
• add some lines for large resid used in PDB by @yskmiyazaki in https://github.com/SPICA-group/spica-tools/pull/15
• Load "dihedral" and "improper" directives in top files and format DATA.FILE by @yskmiyazaki in https://github.com/SPICA-group/spica-tools/pull/14
• Add a new code "gen_lmp_input.py" to generate a basic LAMMPS input file for SPICA by @yskmiyazaki in https://github.com/SPICA-group/spica-tools/pull/16
• Mod/dihed by @yskmiyazaki in https://github.com/SPICA-group/spica-tools/pull/17
• bugfix by @yskmiyazaki in https://github.com/SPICA-group/spica-tools/pull/18
• Dssp by @yamatetsu1102 in https://github.com/SPICA-group/spica-tools/pull/19
• Mod ions by @yskmiyazaki in https://github.com/SPICA-group/spica-tools/pull/20
• collect small fixes by @yskmiyazaki in https://github.com/SPICA-group/spica-tools/pull/21
• update rst files for documentation by @yskmiyazaki in https://github.com/SPICA-group/spica-tools/pull/24

New Contributors

• @onefive13 made their first contribution in https://github.com/SPICA-group/spica-tools/pull/2
• @yamatetsu1102 made their first contribution in https://github.com/SPICA-group/spica-tools/pull/3

Full Changelog: https://github.com/SPICA-group/spica-tools/commits/v1.0.0