HITS-MCM/gromacs-ramd

Issues

• Installation Error

  #33 opened 3 months ago by erolic
  8

• The simulation is not terminated after the ligand has exited the binding site using MPI

  #37 opened 4 months ago by BerndDoser
  0

• The reference atom for periodic boundary conditions will not be considered

  #38 opened 4 months ago by BerndDoser
  1

• how to install RAMD

  #35 opened 7 months ago by bigsmartguy
  0

• "Unknown left-hand 'ramd-force' .... in parameter file"

  #34 opened 8 months ago by wenchangzhou-qtx
  1

• Update to GROMACS 2021 and 2022

  #24 opened a year ago by BerndDoser
  0

• New option `ramd-connected-ligands`

  #29 opened a year ago by BerndDoser
  1

• Synchronized trajectory output

  #30 opened a year ago by BerndDoser
  1

• Acclerating only a part of the ligand

  #28 opened 2 years ago by kellegra
  1

• how do i install ramd when compiling gromacs

  #27 opened 3 years ago by Byun-jinyoung
  1

• ramd MD trajectories look strange

  #25 opened 3 years ago by satvikkg
  3

• A RAMD run is likely not to restart properly.

  #23 opened 3 years ago by physicshinzui
  5

• I am wondering whether parameter names in the README are inconsistent with those in your software?

  #22 opened 3 years ago by physicshinzui
  1

• Last value in pullx- and pullf-file is zero

  #21 opened 3 years ago by BerndDoser
  0

• Write number of steps for every exit event

  #19 opened 3 years ago by BerndDoser
  0

• Remove RAMD forces after ligand has left the binding site

  #20 opened 3 years ago by BerndDoser
  0

• Wrong ligand-receptor distance using PBC

  #18 opened 3 years ago by BerndDoser
  0

• Use ForceProvider interface to apply RAMD forces

  #14 opened 3 years ago by BerndDoser
  0

• Gromacs2020.3-RAMD1.1 error: Aborted (core dumped)

  #13 opened 3 years ago by satvikkg
  5

• Manage multiple binding sites

  #15 opened 3 years ago by BerndDoser
  2

• Treatment of pbc reference atoms

  #16 opened 3 years ago by BerndDoser
  0

• Units for the ramd-inputs

  #17 opened 3 years ago by kellegra
  4

• Use gromacs stop condition after max distance is reached

  #12 opened 4 years ago by BerndDoser
  0

• Write receptor-ligand COM distance to ramd.xvg file

  #10 opened 4 years ago by BerndDoser
  1

• COM distances are zero in pullx-file

  #9 opened 4 years ago by BerndDoser
  0

• Pull direction will not be updated for MPI workers

  #11 opened 4 years ago by BerndDoser
  0

• Add regression test for 1WDHI example

  #7 opened 5 years ago by BerndDoser
  0

• Add documentation of RAMD input

  #8 opened 5 years ago by BerndDoser
  0

• Define new pull external potential provider RAMD and register it for grompp and mdrun

  #6 opened 5 years ago by BerndDoser
  0

• Reuse PULL code for RAMD

  #4 opened 5 years ago by BerndDoser
  0

• Test to reproduce PULL code result with RAMD code

  #5 opened 5 years ago by BerndDoser
  0

• Create RAMD input variables and read them from file md.mdp

  #2 opened 5 years ago by BerndDoser
  0

• Convert index group to atom index list for RAMD protein and ligand

  #3 opened 5 years ago by BerndDoser
  0

• Insert ramd branch for modifying forces as for pull code

  #1 opened 5 years ago by BerndDoser
  1