Amber Archive Jun 2025 by date

84 messages: Starting Tue Jun 03 2025 - 21:30:02 PDT, Ending Mon Jun 30 2025 - 11:00:02 PDT
This period: Most recent messages
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Tuesday, 3 June 2025
- [AMBER] RAMD Dhananjay via AMBER
Wednesday, 4 June 2025
- [AMBER] spc/fw water model Dulal Mondal via AMBER
- Re: [AMBER] spc/fw water model Timothy Giese via AMBER
- Re: [AMBER] spc/fw water model Dulal Mondal via AMBER
- Re: [AMBER] spc/fw water model Dulal Mondal via AMBER
Friday, 6 June 2025
- [AMBER] Possible bug in restraint mask parsing during minimization in AMBER24 (works in AMBER22) Pedro Martínez Zaragoza via AMBER
- Re: [AMBER] Possible bug in restraint mask parsing during minimization in AMBER24 (works in AMBER22) Adrian Roitberg via AMBER
- [AMBER] Steered MD with two variables Kriti Shukla via AMBER
Sunday, 8 June 2025
- [AMBER] Segmentation fault occurred when using Amber with Plumed Jiahua Deng via AMBER
Monday, 9 June 2025
- [AMBER] whether the PM6-DH+ method supports cuda acceleration xurui via AMBER
- [AMBER] Segmentation fault when running TI with lambda scheduling for restraints on AMBER 24 (AMD GPU) Yuxuan Zhuang via AMBER
- Re: [AMBER] whether the PM6-DH+ method supports cuda acceleration David A Case via AMBER
Tuesday, 10 June 2025
- [AMBER] errors in total energy Sudipti Priyadarsinee via AMBER
- Re: [AMBER] errors in total energy Elvis Martis via AMBER
- Re: [AMBER] errors in total energy Carlos Simmerling via AMBER
- [AMBER] Accelerating NMA Calculations in MMPBSA.py for Large Number of Structures Rahul Singal via AMBER
Wednesday, 11 June 2025
- Re: [AMBER] Accelerating NMA Calculations in MMPBSA.py for Large Number of Structures David A Case via AMBER
- [AMBER] TIP3P Water issue with MCPB.py Jasmin Güven via AMBER
- Re: [AMBER] TIP3P Water issue with MCPB.py Li, Zhen via AMBER
- Re: [AMBER] TIP3P Water issue with MCPB.py Jasmin Güven via AMBER
- [AMBER] Can cpptraj calculate electron density for molecular surface? Hòa Lê via AMBER
Thursday, 12 June 2025
- Re: [AMBER] errors in total energy Daniel Roe via AMBER
- [AMBER] Illegal Memory Access Oke, Elizabeth Damilola via AMBER
- Re: [AMBER] Illegal Memory Access Daniel Roe via AMBER
- [AMBER] gaff2.dat Kelly, Katie Lynette via AMBER
- Re: [AMBER] gaff2.dat Christina Bergonzo via AMBER
Friday, 13 June 2025
- [AMBER] Error in saving prmtop of a DNA:RNA hybrid structure Sruthi Sudhakar via AMBER
Saturday, 14 June 2025
- Re: [AMBER] Error in saving prmtop of a DNA:RNA hybrid structure Sruthi Sudhakar via AMBER
Sunday, 15 June 2025
- [AMBER] Number of frames loaded in doing MMPBSA.py Jong Young Joung via AMBER
Monday, 16 June 2025
- [AMBER] Fwd: Number of frames loaded in doing MMPBSA.py Jong Young Joung via AMBER
- [AMBER] Building double bilayer using packmol-memgen Cherry, Kendall via AMBER
- Re: [AMBER] Can cpptraj calculate electron density for molecular surface? Hòa Lê via AMBER
Tuesday, 17 June 2025
- [AMBER] Steered MD - Pulling RNA micro helix from protein's pocket Sidharth E K via AMBER
Wednesday, 18 June 2025
- [AMBER] Recommended barostat for membrane protein simulations? Cherry, Kendall via AMBER
- Re: [AMBER] Recommended barostat for membrane protein simulations? Dickson, Callum via AMBER
- [AMBER] How can I pack a protein (not GPCR) into the centre of bilayer membrane and perpendicular to the xy plane? yumura.seigo967--- via AMBER
Thursday, 19 June 2025
- Re: [AMBER] How can I pack a protein (not GPCR) into the centre of bilayer membrane and perpendicular to the xy plane? Stephan Schott via AMBER
- Re: [AMBER] Building double bilayer using packmol-memgen Stephan Schott via AMBER
- Re: [AMBER] Building double bilayer using packmol-memgen Cherry, Kendall via AMBER
- Re: [AMBER] Recommended barostat for membrane protein simulations? Cherry, Kendall via AMBER
- Re: [AMBER] Recommended barostat for membrane protein simulations? Dickson, Callum via AMBER
- Re: [AMBER] Recommended barostat for membrane protein simulations? Cherry, Kendall via AMBER
- [AMBER] Antechamber and flying ligand problem Pitambar Poudel via AMBER
Friday, 20 June 2025
- Re: [AMBER] Antechamber and flying ligand problem Dr. Anselm Horn via AMBER
- Re: [AMBER] Building double bilayer using packmol-memgen Stephan Schott via AMBER
- Re: [AMBER] Building double bilayer using packmol-memgen Cherry, Kendall via AMBER
Monday, 23 June 2025
- Re: [AMBER] [EXTERNAL] AMBER Digest, Vol 4731, Issue 1 Md Imran Ahmed via AMBER
- Re: [AMBER] [EXTERNAL] AMBER Digest, Vol 4731, Issue 1 Dr. Anselm Horn via AMBER
- [AMBER] MM-GBSA Ven, Wouter van de via AMBER
- Re: [AMBER] Antechamber and flying ligand problem Pitambar Poudel via AMBER
Tuesday, 24 June 2025
- Re: [AMBER] Antechamber and flying ligand problem Dr. Anselm Horn via AMBER
- Re: [AMBER] Antechamber and flying ligand problem Pitambar Poudel via AMBER
- [AMBER] cpptraj: nonbond energies calculated by "energy" and "lie" are not the same Игорь Упоров via AMBER
- Re: [AMBER] cpptraj: nonbond energies calculated by "energy" and "lie" are not the same Daniel Roe via AMBER
- Re: [AMBER] cpptraj: nonbond energies calculated by "energy" and "lie" are not the same Daniel Roe via AMBER
- [AMBER] flatwell restraints MANVENDRA SINGH via AMBER
- Re: [AMBER] flatwell restraints David A Case via AMBER
- Re: [AMBER] [EXTERNAL] AMBER Digest, Vol 4731, Issue 1 David A Case via AMBER
- [AMBER] Getting started with Amber tutorials David A Case via AMBER
Wednesday, 25 June 2025
- [AMBER] Getting different behavior between serial and MPI implementations of Sander Silva Carvalho, Felipe via AMBER
- [AMBER] Failed to build XTB in Amber 24 (missing xtb_xtb_calculator.mod) Chunsheng Lin via AMBER
Thursday, 26 June 2025
- Re: [AMBER] Failed to build XTB in Amber 24 (missing xtb_xtb_calculator.mod) Timothy Giese via AMBER
- [AMBER] Issue with dumpave in adaptive solvent QM/MM umbrella sampling Ameni BEN ABDELJAOUED via AMBER
- Re: [AMBER] Issue with dumpave in adaptive solvent QM/MM umbrella sampling Goetz, Andreas via AMBER
- Re: [AMBER] Antechamber and flying ligand problem Pitambar Poudel via AMBER
Friday, 27 June 2025
- [AMBER] sander.MPI aborted Priyasha Majee via AMBER
- Re: [AMBER] sander.MPI aborted Carlos Simmerling via AMBER
- Re: [AMBER] sander.MPI aborted Téletchéa Stéphane via AMBER
- Re: [AMBER] Recommended barostat for membrane protein simulations? Téletchéa Stéphane via AMBER
- Re: [AMBER] Antechamber and flying ligand problem Dr. Anselm Horn via AMBER
- Re: [AMBER] sander.MPI aborted Carlos Simmerling via AMBER
- Re: [AMBER] Antechamber and flying ligand problem Pitambar Poudel via AMBER
- Re: [AMBER] sander.MPI aborted Priyasha Majee via AMBER
Saturday, 28 June 2025
- Re: [AMBER] Issue with dumpave in adaptive solvent QM/MM umbrella sampling Ameni BEN ABDELJAOUED via AMBER
- Re: [AMBER] sander.MPI aborted David A Case via AMBER
- Re: [AMBER] Getting different behavior between serial and MPI implementations of Sander David A Case via AMBER
- [AMBER] Potential Bug in QM/MM Virial Calculation and Suggestions for Ewald Error Estimation in AMBER ZIHAO BAI via AMBER
- Re: [AMBER] Potential Bug in QM/MM Virial Calculation and Suggestions for Ewald Error Estimation in AMBER ZIHAO BAI via AMBER
- Re: [AMBER] Potential Bug in QM/MM Virial Calculation and Suggestions for Ewald Error Estimation in AMBER David A Case via AMBER
- Re: [AMBER] Potential Bug in QM/MM Virial Calculation and Suggestions for Ewald Error Estimation in AMBER David A Case via AMBER
Sunday, 29 June 2025
- [AMBER] Instability when continuing GPU simulation with Berendsen Barostat on Cluster (A100) Delwakkada Liyanage, Senal Dinuka via AMBER
- Re: [AMBER] Instability when continuing GPU simulation with Berendsen Barostat on Cluster (A100) David A Case via AMBER
Monday, 30 June 2025
- [AMBER] Help with writing the input files for distance and WC Restraints in Amber MANVENDRA SINGH via AMBER
- Re: [AMBER] Help with writing the input files for distance and WC Restraints in Amber Christina Bergonzo via AMBER

Last message date: Mon Jun 30 2025 - 11:00:02 PDT
Archived on: Wed Jul 16 2025 - 05:56:20 PDT