Acellera/htmd

Issues

• Request to Fix Error with 5-Methyl Cytosine amber Force Fields and Suggestion for Improvement

  #1090 opened 5 months ago by vas2201
  15

• Add phosphorylation patch

  #1095 opened a month ago by H-EKE
  4

• inconsistent results for ACEMD 2 and ACEMD 3

  #1088 opened 6 months ago by smar966
  21

• Problems running adaptive MD script

  #1041 opened 2 months ago by smar966
  16

• 3D FES profile

  #1065 opened 2 months ago by vas2201
  1

• Issues with equilibration phase (Protein-RNA-complex)

  #1048 opened 2 months ago by vas2201
  11

• Building a membrane with more than three different lipids

  #1045 opened 2 months ago by Saleh-OM4R
  2

• freshly installed version retuned as expired

  #1044 opened 2 months ago by msturlese2
  1

• Input file options - parameter "exclude"

  #1046 opened 2 months ago by szotkowska-v
  0

• Problem with charmm.build

  #1055 opened 2 months ago by danaeko
  8

• ACEMD3 and RTX4070ti

  #1060 opened 2 months ago by anicoli
  4

• charmm build in htmd 2.3.8

  #1076 opened 2 months ago by shozebhaider
  3

• unable to execute the tutorial

  #1089 opened 2 months ago by pritam0070
  3

• problem in the systemPrepare function with new version

  #1094 opened 3 months ago by matteagle2
  1

• ERROR: syntax error in file "parameters", line number 15733: syntax error in CHARMM nbfix

  #1093 opened 3 months ago by vas2201
  1

• Constant ratio for membrane protein simulations

  #1092 opened 3 months ago by Saleh-OM4R
  1

• Reg : Amber / Charmm Force field parameters for ARG (mono-methyl, dimethyl (asym, sym)

  #1084 opened 5 months ago by vas2201
  4

• Extract Trajectory Without Water and Ions

  #1087 opened 6 months ago by vas2201
  1

• acemd Computation: atomRestraint harmonic caused external energy calculation

  #1086 opened 6 months ago by Jingdan-Chen
  2

• Installation Error: acemd >=2019.01.24 , which does not exist

  #1085 opened 7 months ago by Jingdan-Chen
  2

• Tutorial adaptative sampling

  #1071 opened 7 months ago by H-EKE
  4

• Error : model.viewStates(nucleic=True), not recognize the 'nucleic' parameter

  #1073 opened 7 months ago by vas2201
  5

• Provide simlist with single .psf file for all trajectories

  #1083 opened 8 months ago by AdriaPerezCulubret
  1

• Parameters generated with charm.build on HTMD

  #1077 opened 8 months ago by H-EKE
  0

• Trouble installing: htmd does not exist

  #1080 opened 8 months ago by MarioAsti8
  2

• IndexError: arrays used as indices must be of integer (or boolean) type

  #1079 opened 8 months ago by vas2201
  6

• Issue with model._active_set

  #1075 opened a year ago by antoinekoehl
  1

• MOLECULE DESTROYED BY FATAL ERROR! Use resetpsf to start over.

  #1074 opened a year ago by H-EKE
  4

• Issues with System building for RNA-ligand

  #1050 opened a year ago by vas2201
  13

• Unable to prepare system with charmm FF

  #1069 opened a year ago by smar966
  7

• acemd is failing with cuda version 12.1

  #1072 opened a year ago by vas2201
  1

• ACEMD on multiple nodes and/or GPUs

  #1070 opened a year ago by danaeko
  1

• HTMD not working with GTX1650

  #1067 opened a year ago by khairbux2023
  3

• Registration not working for HTMD3 2022_12_07

  #1068 opened a year ago by honzamican
  3

• Switch from NVT to NPT (Equilibration)

  #1066 opened a year ago by H-EKE
  1

• Co-solvent MD

  #1064 opened a year ago by H-EKE
  3

• No structure pdb/psf file was generated

  #1063 opened a year ago by Grad1029
  2

• systemPrepare add positive charge to HIP and HID

  #1062 opened a year ago by elifzeng
  5

• Conda installation problems

  #1061 opened a year ago by tonigi
  4

• Installation with conda stuck on "Solving Environment"

  #1059 opened a year ago by A-Sethi
  3

• RuntimeError (adaptive MD for RNA): when using a dihedral with an atom name containing a single quote

  #1056 opened 2 years ago by vas2201
  13

• charmm.build problem

  #1057 opened 2 years ago by suice07
  2

• Request for Generating TPR and NDX Files for Protein system Using HTMD

  #1053 opened 2 years ago by vas2201
  6

• parametrization tool

  #1054 opened 2 years ago by mmagithub
  1

• RuntimeError

  #1052 opened 2 years ago by jmroldan1975
  2

• amber.build issues

  #1051 opened 2 years ago by shozebhaider
  2

• How to construct the dihedrals.projections for RNA to include in adaptive MD ?

  #1049 opened 2 years ago by vas2201
  6

• Adaptative MD on local gpu

  #1047 opened 2 years ago by vas2201
  5

• Problems installing HTMD

  #1043 opened 2 years ago by lblaabjerg
  10

• Charmm file error on membrane build

  #1042 opened 2 years ago by shozebhaider
  8