Amber Archive Apr 2023 by date

80 messages: Starting Sat Apr 01 2023 - 08:30:02 PDT, Ending Sun Apr 30 2023 - 05:00:02 PDT
This period: Most recent messages
sort by: [ thread ] [ author ] [ date ] [ subject ] [ attachment ]

Saturday, 1 April 2023
- [AMBER] Introducing ChatGPDB - The Ultimate Biomolecular Simulation Assistant Jason Swails via AMBER
- Re: [AMBER] Introducing ChatGPDB - The Ultimate Biomolecular Simulation Assistant Francesca Mocci via AMBER
- Re: [AMBER] Introducing ChatGPDB - The Ultimate Biomolecular Simulation Assistant Charo del Genio via AMBER
Sunday, 2 April 2023
- [AMBER] compiling amber 22 with gcc 11 / cuda 11.6: cuda error with mdgx Vlad Cojocaru via AMBER
Monday, 3 April 2023
- Re: [AMBER] TI calculation regarding charge change in TI region. Michael T Kim via AMBER
- [AMBER] p5 to C.3 conversion in ATOMTYPE_CHECK.TAB Christopher Corbo via AMBER
Tuesday, 4 April 2023
- [AMBER] Repulsive restraints between two atoms or two groups of atoms Antonio Frances Monerris via AMBER
- Re: [AMBER] Repulsive restraints between two atoms or two groups of atoms Carlos Simmerling via AMBER
- [AMBER] pmemd.cuda test possible failure Freddy Bernal via AMBER
- [AMBER] Internal pyrophosphates with Amber Harvey Dale via AMBER
Wednesday, 5 April 2023
- Re: [AMBER] pmemd.cuda test possible failure David A Case via AMBER
- Re: [AMBER] TI calculation regarding charge change in TI region. Michael T Kim via AMBER
Thursday, 6 April 2023
- [AMBER] Wrong Coordination Number ! angad sharma via AMBER
- [AMBER] MMPBSA help - Sarah Abraham Abraham, Sarah via AMBER
Friday, 7 April 2023
- [AMBER] Thermodynamic property of the system Dulal Mondal via AMBER
- Re: [AMBER] Thermodynamic property of the system David Case via AMBER
- [AMBER] Post-doc position open for one year in my lab in Nantes, France Téletchéa Stéphane via AMBER
- Re: [AMBER] MMPBSA help - Sarah Abraham Bill Miller III via AMBER
- [AMBER] Question about implementing steered MD in Amber SONAL GAHLAWAT via AMBER
Sunday, 9 April 2023
- [AMBER] Coordination Number angad sharma via AMBER
Tuesday, 11 April 2023
- Re: [AMBER] issue with pdb4amber Hai Nguyen via AMBER
- Re: [AMBER] issue with pdb4amber Hai Nguyen via AMBER
- Re: [AMBER] issue with pdb4amber David A Case via AMBER
- Re: [AMBER] issue with pdb4amber Andriy Kovalenko via AMBER
Wednesday, 12 April 2023
- Re: [AMBER] issue with pdb4amber Hai Nguyen via AMBER
- [AMBER] Installing AmberTools18 CHAN LOK YUNG via AMBER
- Re: [AMBER] Installing AmberTools18 SATYAJIT KHATUA via AMBER
- Re: [AMBER] Installing AmberTools18 SATYAJIT KHATUA via AMBER
Thursday, 13 April 2023
- [AMBER] Widom insertion method, calculate chemical potential Alexej Jerschow via AMBER
Monday, 17 April 2023
- [AMBER] Why uinsg a cutoff or 8.0 for proteins and 10.0 for proteins embeded in a membrane? Téletchéa Stéphane via AMBER
- Re: [AMBER] Why uinsg a cutoff or 8.0 for proteins and 10.0 for proteins embeded in a membrane? Téletchéa Stéphane via AMBER
- [AMBER] Why using a cutoff or 8.0 for proteins and 10.0 for proteins embeded in a membrane? Téletchéa Stéphane via AMBER
- Re: [AMBER] [Sender Not Verified] Re: Why uinsg a cutoff or 8.0 for proteins and 10.0 for proteins embeded in a membrane? Steinbrecher, Thomas via AMBER
Tuesday, 18 April 2023
- [AMBER] correlation matrix Dulal Mondal via AMBER
- Re: [AMBER] [Sender Not Verified] correlation matrix Steinbrecher, Thomas via AMBER
Wednesday, 19 April 2023
- [AMBER] constant ph calculations Hoang, Oanh Tu via AMBER
- Re: [AMBER] constant ph calculations Vinicius Wilian Cruzeiro via AMBER
- [AMBER] Restraints not read by Sander for QM/MM Abdullah Bin Faheem via AMBER
- Re: [AMBER] Restraints not read by Sander for QM/MM Carlos Simmerling via AMBER
- Re: [AMBER] Restraints not read by Sander for QM/MM Abdullah Bin Faheem via AMBER
- Re: [AMBER] Restraints not read by Sander for QM/MM Carlos Simmerling via AMBER
- Re: [AMBER] Restraints not read by Sander for QM/MM David A Case via AMBER
Thursday, 20 April 2023
- Re: [AMBER] Restraints not read by Sander for QM/MM Abdullah Bin Faheem via AMBER
- [AMBER] Question about "nfft1 must be in the range of 6 to 512!" Dr. Anselm Horn via AMBER
Friday, 21 April 2023
- Re: [AMBER] Question about "nfft1 must be in the range of 6 to 512!" Dr. Anselm Horn via AMBER
- [AMBER] Help in determining no. of molecules for ionic liquid Delwakkada Liyanage, Senal Dinuka via AMBER
Sunday, 23 April 2023
- [AMBER] Separating a trajectory by output from clusterdihedral Osman, Roman via AMBER
- Re: [AMBER] {SPAM?} Separating a trajectory by output from clusterdihedral Matthew Guberman-Pfeffer via AMBER
- Re: [AMBER] {SPAM?} Separating a trajectory by output from clusterdihedral Osman, Roman via AMBER
- Re: [AMBER] Separating a trajectory by output from clusterdihedral Daniel Roe via AMBER
- Re: [AMBER] [Sender Not Verified] Help in determining no. of molecules for ionic liquid Steinbrecher, Thomas via AMBER
Monday, 24 April 2023
- [AMBER] Not able to reproduce MMPBSA values using data from the tutorial devendra.prajapat.cys19--- via AMBER
- [AMBER] Using atom OD with parmchk and ff15ipq amin sagar via AMBER
- [AMBER] Query regarding atomicfluct command Roy, Rajarshi via AMBER
- Re: [AMBER] Query regarding atomicfluct command SATYAJIT KHATUA via AMBER
- Re: [AMBER] Not able to reproduce MMPBSA values using data from the tutorial Ray Luo via AMBER
- Re: [AMBER] Query regarding atomicfluct command SATYAJIT KHATUA via AMBER
- Re: [AMBER] Query regarding atomicfluct command SATYAJIT KHATUA via AMBER
- Re: [AMBER] Query regarding atomicfluct command SATYAJIT KHATUA via AMBER
- Re: [AMBER] Query regarding atomicfluct command Thomas Cheatham via AMBER
- Re: [AMBER] Query regarding atomicfluct command Roy, Rajarshi via AMBER
- Re: [AMBER] Query regarding atomicfluct command Faezeh Salehi via AMBER
- [AMBER] density input Andriy Kovalenko via AMBER
- Re: [AMBER] density input David Case via AMBER
Tuesday, 25 April 2023
- [AMBER] Restraining Counterions in Regular MD Simulations Rory Crean via AMBER
- Re: [AMBER] Using atom OD with parmchk and ff15ipq Carlos Simmerling via AMBER
- [AMBER] Using atom OD with parmchk and ff15ipq aamin.sagar--- via AMBER
- Re: [AMBER] Restraining Counterions in Regular MD Simulations Christina Bergonzo via AMBER
- Re: [AMBER] Restraining Counterions in Regular MD Simulations David A Case via AMBER
- Re: [AMBER] Query regarding atomicfluct command Faezeh Salehi via AMBER
Wednesday, 26 April 2023
- [AMBER] cphstats in CpHMD analysis Dulal Mondal via AMBER
- Re: [AMBER] Restraining Counterions in Regular MD Simulations Rory Crean via AMBER
- [AMBER] Fwd: Query regarding restarting the replica exchange molecular dynamics simulation Munazzah Fatima Ansari via AMBER
- [AMBER] Multisander, Vilhelm Ekberg via AMBER
- [AMBER] amber19 compilation Dulal Mondal via AMBER
- Re: [AMBER] amber19 compilation David A Case via AMBER
Friday, 28 April 2023
- Re: [AMBER] cphstats in CpHMD analysis Jason Swails via AMBER
- [AMBER] taking Center of mass of 2 atoms in umbrella sampling angad sharma via AMBER
Saturday, 29 April 2023
- [AMBER] protonation state of a residue e.g. Histidine Dulal Mondal via AMBER
Sunday, 30 April 2023
- [AMBER] Release of AmberTools23 David A Case via AMBER

Last message date: Sun Apr 30 2023 - 05:00:02 PDT
Archived on: Mon Feb 03 2025 - 05:56:10 PST