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Feature #2308

Feature #2307: Implement MiMiC-based QM/MM functionality in GROMACS

Implement QM/MM updates in GROMACS preprocessor

Added by Viacheslav Bolnykh almost 2 years ago. Updated 11 months ago.

Status:
Closed
Priority:
Normal
Category:
preprocessing (pdb2gmx,grompp)
Target version:
Difficulty:
hard
Close

Description

In order to support the new QM/MM workflow developed within BioExcel (working name MiMiC) we need to implement new features in the preprocessor.

  1. Additional group to define QM/MM atoms (to avoid overlap with an old QM/MM code)
  2. New input file section mimic-grps of type string - to define the QM group
  3. Modifications of options in QMMM section: no (no QM/MM), yes (original QM/MM implementation), mimic (MiMiC QM/MM interface)
  4. Zeroing charges of QM atoms
  5. Update the intra-molecular exclusion lists
  6. Replace bonds between QM atoms with CONNBOND
  7. Add tests for the new functionality

Associated revisions

Revision 61e7a6a1 (diff)
Added by Viacheslav Bolnykh 11 months ago

Implemented changes to preprocessor to work with MiMiC QM/MM

Added new integrator "mimic" and updated usage of QMMM-grps to be used
with MiMiC QM/MM. Updated code zeros charges within QM region and
changes bonds to CONNBOND and updates exclusion lists to exclude
non-bonded interactions between quantum atoms

Refs #2308

Change-Id: I34e798ae0c54457dad8f9a8f220482468db34708

History

#1 Updated by Aleksei Iupinov almost 2 years ago

  • Parent task set to #2307

#2 Updated by Mark Abraham almost 2 years ago

  • Target version changed from 2018 to 2019

#3 Updated by Gerrit Code Review Bot over 1 year ago

Gerrit received a related DRAFT patchset '1' for Issue #2308.
Uploader: Viacheslav Bolnykh ()
Change-Id: gromacs~master~I34e798ae0c54457dad8f9a8f220482468db34708
Gerrit URL: https://gerrit.gromacs.org/7434

#4 Updated by Mark Abraham 12 months ago

  • Status changed from New to Fix uploaded

#5 Updated by Mark Abraham 11 months ago

  • Status changed from Fix uploaded to Resolved

#6 Updated by Mark Abraham 11 months ago

  • Status changed from Resolved to Closed

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