Amber Archive Aug 2023: by subject

[AMBER] [Sender Not Verified] gamma_ln in simulated annealing
- Steinbrecher, Thomas via AMBER (Sun Aug 27 2023 - 23:40:40 PDT)
[AMBER] [Sender Not Verified] Regarding error in the tleap output file
- Steinbrecher, Thomas via AMBER (Tue Aug 22 2023 - 01:22:38 PDT)
[AMBER] Adding new atom type in PARMCHK.DAT
- Dr. Anselm Horn via AMBER (Wed Aug 30 2023 - 01:04:27 PDT)
- Priyasha Majee via AMBER (Mon Aug 28 2023 - 07:23:02 PDT)
[AMBER] Aligning MD snapshots excluding loops
- Daniel Roe via AMBER (Wed Aug 02 2023 - 07:17:19 PDT)
[AMBER] Amber problem looking for help
- leveen via AMBER (Thu Aug 03 2023 - 18:54:30 PDT)
[AMBER] Applying external electric field in the simulation
- Markowska (Thu Aug 24 2023 - 02:27:57 PDT)
- Markowska (Wed Aug 23 2023 - 03:56:25 PDT)
[AMBER] ATTN, need revision
- He, Amy via AMBER (Thu Aug 31 2023 - 07:50:52 PDT)
- Priyasha Majee via AMBER (Thu Aug 31 2023 - 01:16:15 PDT)
- He, Amy via AMBER (Wed Aug 30 2023 - 08:15:37 PDT)
- Priyasha Majee via AMBER (Wed Aug 30 2023 - 04:08:57 PDT)
[AMBER] Benchmarks for new NVIDIA cards?
- Tucker Burgin via AMBER (Tue Aug 22 2023 - 11:21:17 PDT)
[AMBER] Blank frcmod file is generating
- Daniel Roe via AMBER (Fri Aug 18 2023 - 08:33:27 PDT)
- KAJAL ABROL via AMBER (Thu Aug 17 2023 - 22:14:57 PDT)
[AMBER] Compiling AMBER23
- accuratefreeenergy--- via AMBER (Tue Aug 29 2023 - 03:50:12 PDT)
- SATYAJIT KHATUA via AMBER (Mon Aug 28 2023 - 21:32:59 PDT)
- Javier O Sanlley-hernandez via AMBER (Mon Aug 28 2023 - 16:22:19 PDT)
[AMBER] constant pH MD constant pressure ERROR Amber 22
- Mahdi Hassankalhori via AMBER (Thu Aug 03 2023 - 03:30:54 PDT)
[AMBER] CpHMD run in explicit solvent in cuda
- Jason Swails via AMBER (Tue Aug 29 2023 - 08:40:50 PDT)
- Dulal Mondal via AMBER (Tue Aug 29 2023 - 00:19:33 PDT)
- Dulal Mondal via AMBER (Mon Aug 28 2023 - 23:17:15 PDT)
[AMBER] CpHMD, membrane proteins
- Matthew Guberman-Pfeffer via AMBER (Fri Aug 04 2023 - 14:49:38 PDT)
[AMBER] cpptraj: offset option for trajout
- Enrico Martinez via AMBER (Wed Aug 30 2023 - 03:36:17 PDT)
[AMBER] Cross Correlation Analysis
- Shah, Tejas V. via AMBER (Thu Aug 31 2023 - 13:21:45 PDT)
[AMBER] DNA with two ligand molecules for MD
- maya nair via AMBER (Sat Aug 05 2023 - 05:12:21 PDT)
[AMBER] Error in energy minimization step
- Carlos Simmerling via AMBER (Wed Aug 30 2023 - 06:15:01 PDT)
- KAJAL ABROL via AMBER (Wed Aug 30 2023 - 05:59:45 PDT)
[AMBER] Error running minimization
- Ritwika Chatterjee via AMBER (Mon Aug 07 2023 - 04:46:43 PDT)
[AMBER] Error: Fast 3-point water residue, name and bond data incorrect!
- Carlos Simmerling via AMBER (Wed Aug 23 2023 - 04:30:53 PDT)
- Carlos Simmerling via AMBER (Wed Aug 16 2023 - 07:23:13 PDT)
- Derek M Shore via AMBER (Tue Aug 15 2023 - 17:18:59 PDT)
[AMBER] Extract energy change contribution for specific mutation from TI simulation.
- Fanyu Zhao via AMBER (Tue Aug 01 2023 - 03:38:49 PDT)
[AMBER] Fwd: H-bond analysis
- Neelanjana via AMBER (Wed Aug 30 2023 - 02:26:18 PDT)
[AMBER] gamma_ln in simulated annealing
- Anirban Ghosh via AMBER (Sat Aug 26 2023 - 05:24:59 PDT)
[AMBER] H-bond analysis
- Neelanjana via AMBER (Tue Aug 29 2023 - 23:47:15 PDT)
[AMBER] How to place extra point of charge to simulate sigma hole on halogens
- Friederike Leßmöllmann via AMBER (Mon Aug 28 2023 - 12:27:03 PDT)
[AMBER] Input file for Curve+
- angad sharma via AMBER (Sat Aug 05 2023 - 12:57:27 PDT)
[AMBER] Issue with deprecated np.float when using packmol-memgen
- Damas Joao CHST via AMBER (Tue Aug 08 2023 - 06:57:49 PDT)
- Stephan Schott via AMBER (Tue Aug 08 2023 - 06:50:42 PDT)
- Damas Joao CHST via AMBER (Tue Aug 08 2023 - 02:26:09 PDT)
[AMBER] LEaP scripting
- Dr. Anselm Horn via AMBER (Sat Aug 19 2023 - 03:49:12 PDT)
- amber--- via AMBER (Fri Aug 18 2023 - 09:17:42 PDT)
[AMBER] Local structure index )LSI) help
- Zafar,Muhammad Saqlain via AMBER (Wed Aug 02 2023 - 23:04:21 PDT)
[AMBER] Membrane protein tutorial: dimensions of the system
- Enrico Martinez via AMBER (Thu Aug 31 2023 - 06:24:32 PDT)
[AMBER] minimisation with pmemd.cuda
- Enrico Martinez via AMBER (Thu Aug 24 2023 - 08:07:04 PDT)
[AMBER] MMPBSA-error:
- SATYAJIT KHATUA via AMBER (Thu Aug 17 2023 - 01:48:48 PDT)
- Kankana Bhattacharjee via AMBER (Thu Aug 17 2023 - 01:36:13 PDT)
[AMBER] MMPBSA-Nonpolar-solvation-energy-parameters:
- Ray Luo via AMBER (Tue Aug 29 2023 - 14:37:17 PDT)
- Kankana Bhattacharjee via AMBER (Mon Aug 28 2023 - 22:41:36 PDT)
- Kankana Bhattacharjee via AMBER (Mon Aug 28 2023 - 12:09:55 PDT)
- Ray Luo via AMBER (Mon Aug 28 2023 - 10:54:01 PDT)
- Kankana Bhattacharjee via AMBER (Mon Aug 28 2023 - 10:15:03 PDT)
- Ray Luo via AMBER (Mon Aug 28 2023 - 08:46:35 PDT)
- Kankana Bhattacharjee via AMBER (Mon Aug 28 2023 - 05:09:39 PDT)
- Ray Luo via AMBER (Sun Aug 27 2023 - 22:13:03 PDT)
- Kankana Bhattacharjee via AMBER (Sun Aug 27 2023 - 20:25:30 PDT)
- Ray Luo via AMBER (Sun Aug 27 2023 - 16:12:51 PDT)
- Ray Luo via AMBER (Sat Aug 26 2023 - 22:43:22 PDT)
- Kankana Bhattacharjee via AMBER (Fri Aug 25 2023 - 12:47:27 PDT)
[AMBER] Parallel AmberTools Build Error: mpi4py.MPI fails to build
- Hai Nguyen via AMBER (Thu Aug 03 2023 - 07:15:20 PDT)
- Hai Nguyen via AMBER (Thu Aug 03 2023 - 05:52:32 PDT)
- Meyer, Olivia \(meyerok\) via AMBER (Wed Aug 02 2023 - 10:58:28 PDT)
[AMBER] Paths with spaces in cpptraj
- Carlos Simmerling via AMBER (Tue Aug 29 2023 - 13:16:42 PDT)
- Carlos Simmerling via AMBER (Fri Aug 25 2023 - 13:52:50 PDT)
- Mark Mackey via AMBER (Fri Aug 25 2023 - 09:40:29 PDT)
[AMBER] Position Announcement: Postdoctoral Scientist Opportunity
- accuratefreeenergy--- via AMBER (Thu Aug 10 2023 - 08:36:06 PDT)
[AMBER] Probability density with respect to Local structure index (LSI)
- Zafar,Muhammad Saqlain via AMBER (Thu Aug 03 2023 - 10:22:06 PDT)
- Adrian Roitberg via AMBER (Thu Aug 03 2023 - 10:03:50 PDT)
- Zafar,Muhammad Saqlain via AMBER (Thu Aug 03 2023 - 09:03:43 PDT)
[AMBER] Problem with time records in cpout- files in REMD CpHMD simulation
- Elvira Tarasova via AMBER (Fri Aug 11 2023 - 15:27:58 PDT)
- Elvira Tarasova via AMBER (Fri Aug 11 2023 - 14:50:06 PDT)
- Elvira Tarasova via AMBER (Fri Aug 11 2023 - 11:13:19 PDT)
- Elvira Tarasova via AMBER (Thu Aug 10 2023 - 09:41:16 PDT)
- Elvira Tarasova via AMBER (Tue Aug 08 2023 - 11:45:24 PDT)
- Elvira Tarasova via AMBER (Fri Aug 04 2023 - 13:50:15 PDT)
[AMBER] Problems with post-processing MD simulation with non-standard residues
- Daniel Roe via AMBER (Sat Aug 12 2023 - 17:57:43 PDT)
- Daniel Roe via AMBER (Sat Aug 12 2023 - 05:29:33 PDT)
- m.bzowka m.bzowka via AMBER (Sat Aug 12 2023 - 01:41:49 PDT)
[AMBER] QMMM-FEP with sander.MPI
- King Wu via AMBER (Wed Aug 16 2023 - 07:50:39 PDT)
- 东庚 via AMBER (Tue Aug 08 2023 - 17:42:01 PDT)
- 东庚 via AMBER (Tue Aug 08 2023 - 17:31:12 PDT)
[AMBER] Query regarding re-weighting in GaMD
- Munazzah Fatima Ansari via AMBER (Thu Aug 10 2023 - 00:15:23 PDT)
[AMBER] Question about Zinc ions
- Sayan Poddar via AMBER (Sat Aug 05 2023 - 04:22:47 PDT)
- Ramachandran, Balajee via AMBER (Sat Aug 05 2023 - 04:17:19 PDT)
- Sayan Poddar via AMBER (Fri Aug 04 2023 - 23:29:36 PDT)
[AMBER] Question regarding PBC simulations with ions
- shiyu wang via AMBER (Wed Aug 23 2023 - 21:45:17 PDT)
- Prithviraj Nandigrami via AMBER (Wed Aug 23 2023 - 12:57:37 PDT)
[AMBER] questions about AmberTools installation from source
- Stephan Schott via AMBER (Mon Aug 21 2023 - 03:03:45 PDT)
- Damas Joao CHST via AMBER (Mon Aug 21 2023 - 02:02:52 PDT)
- Stephan Schott via AMBER (Wed Aug 09 2023 - 04:13:51 PDT)
- Damas Joao CHST via AMBER (Wed Aug 09 2023 - 01:37:51 PDT)
[AMBER] Regarding dU Force Field
- Christina Bergonzo via AMBER (Wed Aug 09 2023 - 05:50:44 PDT)
- Priyasha Majee via AMBER (Wed Aug 09 2023 - 00:16:30 PDT)
[AMBER] Regarding error in the tleap output file
- KAJAL ABROL via AMBER (Sat Aug 19 2023 - 05:09:22 PDT)
[AMBER] Regarding the compatibility of OL15 with protein-RNA-DNA complexes
- Sruthi Sudhakar via AMBER (Wed Aug 09 2023 - 23:45:05 PDT)
[AMBER] Regarding-MMPBSA:
- Kankana Bhattacharjee via AMBER (Wed Aug 16 2023 - 04:58:10 PDT)
[AMBER] Run problem in constant pH REMD in amber22 with pmemd.cuda.MPI in explicit solvent
- Dulal Mondal via AMBER (Wed Aug 23 2023 - 08:01:40 PDT)
- Vinicius Wilian Cruzeiro via AMBER (Wed Aug 23 2023 - 07:53:17 PDT)
- Dulal Mondal via AMBER (Wed Aug 23 2023 - 06:26:44 PDT)
[AMBER] Scientific Question_Debugging
- Dr. Anselm Horn via AMBER (Sun Aug 06 2023 - 06:07:56 PDT)
- Maryam Foroozmehr via AMBER (Thu Aug 03 2023 - 13:46:26 PDT)
- Adrian Roitberg via AMBER (Thu Aug 03 2023 - 13:49:23 PDT)
- Adrian Roitberg via AMBER (Thu Aug 03 2023 - 10:01:20 PDT)
- Maryam Foroozmehr via AMBER (Thu Aug 03 2023 - 09:55:35 PDT)
[AMBER] SHAKE cannot be accomplished?
- Carlos Simmerling via AMBER (Wed Aug 09 2023 - 14:05:26 PDT)
- Debarati DasGupta via AMBER (Wed Aug 09 2023 - 13:58:04 PDT)
[AMBER] simulated annealing of DNA-ligand complex using NMR restrain
- Carlos Simmerling via AMBER (Wed Aug 23 2023 - 12:17:35 PDT)
- Anirban Ghosh via AMBER (Wed Aug 23 2023 - 11:35:34 PDT)
[AMBER] Simulation error when using pmemd.cuda
- Rodrigo Galindo-Murillo via AMBER (Mon Aug 21 2023 - 12:37:39 PDT)
- Loftus, Alec via AMBER (Mon Aug 21 2023 - 11:57:20 PDT)
[AMBER] sqm/mm FEP problem with lambda setting
- leveen via AMBER (Sat Aug 05 2023 - 17:43:59 PDT)
[AMBER] Tetrahedral Order Parameter Q
- SATYAJIT KHATUA via AMBER (Wed Aug 16 2023 - 00:54:31 PDT)
- SATYAJIT KHATUA via AMBER (Wed Aug 16 2023 - 00:35:30 PDT)
- Zafar,Muhammad Saqlain via AMBER (Wed Aug 16 2023 - 00:33:16 PDT)
[AMBER] the charges and atom numbers are mismatch for the standard model!
- Emilie Gerard via AMBER (Sat Aug 12 2023 - 10:05:06 PDT)
[AMBER] The conversion between V and kcal/(mol*A*e) in external electric field.
- 郭家藩 via AMBER (Tue Aug 01 2023 - 08:30:01 PDT)
[AMBER] Trouble installing MPI version - ./configure_mpich not found
- Kovács Richárd Dezső via AMBER (Tue Aug 22 2023 - 03:25:05 PDT)
[AMBER] Warning in compilation: integer conversion resulted in change of sign
- Marcos Verissimo Alves via AMBER (Mon Aug 14 2023 - 05:51:29 PDT)
[AMBER] weird simulation behavior when iwrap=1
- Delwakkada Liyanage, Senal Dinuka via AMBER (Thu Aug 03 2023 - 19:11:18 PDT)
[AMBER] Wrong results when using 4070Ti GPU
- Wang, Yin via AMBER (Mon Aug 07 2023 - 00:41:17 PDT)
[AMBER] Zinc ions bonded with Glutamic acid
- Sayan Poddar via AMBER (Tue Aug 22 2023 - 12:37:28 PDT)

Amber Archive Aug 2023 by subject