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Feature #2307

Implement MiMiC-based QM/MM functionality in GROMACS

Added by Viacheslav Bolnykh over 1 year ago. Updated 7 months ago.

Status:
Closed
Priority:
Normal
Category:
-
Target version:
Difficulty:
hard
Close

Description

Within BioExcel project we are tasked to develop a new QM/MM interface between GROMACS and CPMD. The new interface is done using Multiple-Program Multiple-Data approach. Within this strategy both CPMD and GROMACS are running in parallel independently. GROMACS is used as an MM force provider in this framework. In the beginning of a timestep GROMACS receives the set of coordinates, computes forces and potential energy and sends them to CPMD. CPMD is handling the QM forces as well as the integration and thermostats.

In order to achieve that a number of things has to be done:
  1. Zero charges in the QM region of GROMACS (to avoid double-counting of electrostatics)
  2. Remove LJ interactions between QM atoms (modification of exclusion lists)

This would require the modification of the GROMACS preprocessor to zero charges and modify intra-molecular exclusion lists.
Moreover, additional changes in core GROMACS are required. First, we need to implement inter-molecular exclusions of non-bonded interactions of QM atoms with QM atoms. Then, additional work is needed to implement the MiMiC protocol (see attached pdf document)

protocol_doc.pdf (227 KB) protocol_doc.pdf Description of MiMiC protocol Viacheslav Bolnykh, 11/28/2017 12:47 PM

Subtasks

Feature #2308: Implement QM/MM updates in GROMACS preprocessorClosedViacheslav Bolnykh
Feature #2309: Implement MiMiC QM/MM workflow in the GROMACS coreClosedViacheslav Bolnykh
Task #2690: relax new dependency cycleClosed
Feature #2691: MiMiC needs reference documentationClosed

History

#1 Updated by Viacheslav Bolnykh over 1 year ago

For some reason I cannot set the relations between issues but this is the parent issue to issues #2308 and #2309

#2 Updated by Mark Abraham over 1 year ago

  • Target version changed from 2018 to 2019

#3 Updated by Mark Abraham 9 months ago

  • Status changed from New to In Progress

#4 Updated by Mark Abraham 7 months ago

  • Subject changed from Implememnt the QM/MM functionality in GROMACS to Implement MiMiC-based QM/MM functionality in GROMACS

#5 Updated by Mark Abraham 7 months ago

  • Status changed from In Progress to Fix uploaded

#6 Updated by Paul Bauer 7 months ago

  • Status changed from Fix uploaded to Closed

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