Gallicchio-Lab/AToM-OpenMM

Issues

• Issue: make_atm_system_from_pdb.py loads too many atoms for specified ligand residue ID from PDB

  #98 opened 4 months ago by FlorisLoffler
  5

• Question: ABFE simulation stability dependent on the displacement vector

  #95 opened 5 months ago by hjuinj
  15

• Question: Control file description issues

  #97 opened 5 months ago by FlorisLoffler
  0

• Question: parallelisation of replica exchange on CPU

  #96 opened 5 months ago by FlorisLoffler
  10

• Failed to run ATM with mm/nnp

  #79 opened 6 months ago by RenlingHu
  6

• questions on RBFE examples

  #85 opened 6 months ago by blakemertz
  4

• The problem with pymbar analysis.

  #87 opened 6 months ago by 9527567
  3

• Compatibility with CustomNonBonded Forces from *.xml file

  #91 opened 6 months ago by hongsrich
  1

• Change ligand position restraint

  #93 opened 6 months ago by syxchen
  1

• Question: Can multiple repeats of simulation be aggregated to get better free energy estimates?

  #94 opened 6 months ago by hjuinj
  5

• explicit setting for RBFE simulation length instead of wallclock

  #82 opened a year ago by blakemertz
  4

• Confused about lenght of run

  #83 opened 8 months ago by GattiMh
  1

• Choice of reference atoms

  #89 opened 8 months ago by egallicc
  1

• Question about the units used in AToM

  #92 opened 8 months ago by syxchen
  1

• Positive ABFE result

  #90 opened 9 months ago by nonsensejoke
  2

• Gibbs or Helmholtz free energy in final result?

  #88 opened 9 months ago by smutao
  2

• question about temoa-g1 example result

  #86 opened 10 months ago by camattelaer
  2

• CUDA error: unsupported PTX version

  #84 opened 10 months ago by blakemertz
  2

• No compute devices are alive. Quitting.

  #81 opened a year ago by kong0706
  2

• Doubts about replica exchange.

  #80 opened a year ago by 9527567
  4

• setup-setttings.sh modification.

  #71 opened a year ago by sobertie
  1

• ligand only transformations with changing charge

  #78 opened a year ago by agoliaei
  4

• Proposal: Position-based restraints for the binding pocket

  #77 opened a year ago by stefdoerr
  4

• Aromatic ring explosions during equilibration

  #76 opened a year ago by stefdoerr
  3

• Bug: Config parser and single numbers

  #75 opened a year ago by stefdoerr
  2

• Error when Running Tutorial

  #74 opened a year ago by jianmingm
  4

• No such file or directory

  #62 opened a year ago by sobertie
  3

• Cannot convert from 'angstrom' to 'dimensionless'

  #64 opened a year ago by sobertie
  2

• Are there any published comparisons to other RBFE methods in terms of speed / efficiency?

  #66 opened a year ago by DreamCykl
  9

• MD crash with v8.1.0

  #68 opened a year ago by smutao
  1

• Continuing discussion on speed.

  #69 opened a year ago by 9527567
  5

• The parameters for dynamic sampling and analysis are different in ABFE temoa-g1.

  #70 opened a year ago by 9527567
  2

• AToM fails to detect cuda device temoa1 ABFE example

  #67 opened a year ago by blakemertz
  2

• about alchemical scheme parameters in control file

  #65 opened a year ago by smutao
  2

• Is ligand alignment in the initial state necessary in RBFE?

  #63 opened a year ago by 9527567
  7

• Disconnected alchemical path

  #47 opened a year ago by egallicc
  2

• TypeError: object of type 'NoneType' has no len()

  #53 opened a year ago by sobertie
  4

• Invalid paramerter name: ATMAcore

  #45 opened a year ago by sobertie
  5

• mintherm_template.py and equil_template.py need changes

  #49 opened a year ago by sobertie
  2

• cd: too many arguments

  #54 opened a year ago by sobertie
  2

• Would you consider licensing this code under the MIT License to be consistent with OpenMM?

  #57 opened a year ago by jchodera
  2

• What does LIGOFFSET mean?

  #61 opened a year ago by 9527567
  2

• Can we use MPI to distribute computing?

  #59 opened a year ago by 9527567
  2

• Incorrect progress reporting on GPUGRID - proposed fix

  #46 opened a year ago by Svennemans
  0

• List index out of range

  #52 opened a year ago by sobertie
  0

• Do you have any plans to include other restraints methods in the configuration file？

  #51 opened a year ago by 9527567
  2

• Is it necessary to customize the following parameters for different systems?

  #48 opened a year ago by 9527567
  2

• How to understand Rplots.pdf?

  #42 opened a year ago by 9527567
  7

• Name ATMForce not found

  #44 opened a year ago by sobertie
  0

• About LIGAND1/2_CM_ATOMS

  #39 opened 2 years ago by smutao
  2