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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 about 1 year 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 about 1 year 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 almost 2 years 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 about 1 year ago

  • Status changed from New to Fix uploaded

#5 Updated by Mark Abraham about 1 year ago

  • Status changed from Fix uploaded to Resolved

#6 Updated by Mark Abraham about 1 year ago

  • Status changed from Resolved to Closed

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