Amber Archive Dec 2016 by thread
- [AMBER] Collective Variable not "Strictly" Enforced: Adaptively Biased MD Simulations of type "COM_ANGLE" using "FLOODING" Emmanuel (Wed Nov 30 2016 - 22:08:29 PST)
- [AMBER] clustering doubt Mary Varughese (Wed Nov 30 2016 - 23:26:29 PST)
- [AMBER] Atom type for middle nitrogen in dycyanamide? Mohd Farid Ismail (Thu Dec 01 2016 - 00:59:47 PST)
- [AMBER] question about pol_h in ambertool15 Thibaud von Erlach (Thu Dec 01 2016 - 02:30:32 PST)
- Re: [AMBER] Fw: Problems with imaging Mark Waterhouse [RPG] (Thu Dec 01 2016 - 03:37:35 PST)
- [AMBER] trajectory analysis Carlos Romero (Thu Dec 01 2016 - 22:39:53 PST)
- [AMBER] multiple residues and solvatebox command Azade Yazdan Yar (Fri Dec 02 2016 - 04:24:22 PST)
- [AMBER] Slowly reducing restraints Dd H (Fri Dec 02 2016 - 05:28:05 PST)
- Re: [AMBER] cpptraj - trouble with autoimage and triclinic truncated octahedron DCD from NAMD Brian Radak (Fri Dec 02 2016 - 13:47:45 PST)
- [AMBER] ReCpHMD Optimal values of ntcnstph, ntrelax, nstlim and numexchg Fabrício Bracht (Mon Dec 05 2016 - 04:46:15 PST)
- [AMBER] CpHMD tutorial: how to generate the titration_curves.dat file in an automated way Eric Lang (Mon Dec 05 2016 - 08:36:38 PST)
- Re: [AMBER] Paramfit for multiple molecules Robin Betz (Mon Dec 05 2016 - 16:56:00 PST)
- [AMBER] MMGBSA vs MMPBSA Aronica, Pietro (Mon Dec 05 2016 - 20:10:48 PST)
- [AMBER] Parmchk2 and dihedral parameters Andreas Gavrielides (Tue Dec 06 2016 - 02:28:37 PST)
- [AMBER] How to turn off non-bonded interactions A kS (Tue Dec 06 2016 - 03:36:43 PST)
- Re: [AMBER] Paramfit for multiple molecules (Robin Betz) Sven Hackbusch (Tue Dec 06 2016 - 13:44:35 PST)
- [AMBER] Amber 16: ** NFE-Error ** : Cannot read &colvar namelist! Ruth Helena Tichauer (Wed Dec 07 2016 - 04:32:09 PST)
- [AMBER] Explicit solvent CpHMD calculation with Amber14 Tsibela German Tebello Mofokeng (Wed Dec 07 2016 - 05:23:24 PST)
- [AMBER] The AmberTools 16 build errors Juwen (Wed Dec 07 2016 - 16:35:23 PST)
- [AMBER] Query regarding Ligand Binding Metalloprotein with MCPB.py Abhilash J (Wed Dec 07 2016 - 21:34:21 PST)
- [AMBER] Parallel installation of MMPBSA.py.MPI failed MOHD HOMAIDUR RAHMAN (Thu Dec 08 2016 - 02:03:37 PST)
- [AMBER] NADH antechamber Andreas Tosstorff (Thu Dec 08 2016 - 07:45:17 PST)
- [AMBER] QM/MM/MD g09 interface issues, David Poole (Thu Dec 08 2016 - 08:01:14 PST)
- [AMBER] Installation of AMBER on Centos Rocks 6.2 Yasir Israr (Thu Dec 08 2016 - 18:23:09 PST)
- [AMBER] Fitting of rms2d Mike Nemec (Fri Dec 09 2016 - 05:56:23 PST)
- [AMBER] Eigenvector visualization in Nmode JPB (Fri Dec 09 2016 - 07:32:36 PST)
- [AMBER] HMR with ParmEd for PSF/PDB inputs? Brian Radak (Fri Dec 09 2016 - 07:59:21 PST)
- [AMBER] Freeze Atoms in Nab The Cromicus Productions (Fri Dec 09 2016 - 13:05:12 PST)
- [AMBER] error 睿 ? (Fri Dec 09 2016 - 18:11:09 PST)
- [AMBER] 10. QM/MM/MD g09 interface issues, now tleap David Poole (Sun Dec 11 2016 - 10:42:03 PST)
- [AMBER] Questions regarding Installation of AMBER 16 James Kress (Sun Dec 11 2016 - 13:07:50 PST)
- [AMBER] [Amber] Calculation of Velocity Autocorrelation Function The Cromicus Productions (Sun Dec 11 2016 - 14:10:04 PST)
- [AMBER] Untwisting a molecule The Cromicus Productions (Sun Dec 11 2016 - 14:50:07 PST)
- [AMBER] different frequencies for mdout/mdinfo writes? Bill Ross (Sun Dec 11 2016 - 17:13:42 PST)
- [AMBER] Magnesium ion and MMPBSA/GBSA Francesco Gentile (Sun Dec 11 2016 - 23:44:04 PST)
- [AMBER] AmberTools16 installation problem a.jarmula.nencki.gov.pl (Mon Dec 12 2016 - 04:19:52 PST)
- [AMBER] acdoctor: Warning: There are no hydrogen and halogens in this molecule, it is highly possible that this molecule has open valence Andreas Tosstorff (Mon Dec 12 2016 - 05:12:11 PST)
- [AMBER] Editing residue in PDB file Nikolay N. Kuzmich (Mon Dec 12 2016 - 07:03:56 PST)
- [AMBER] pka of CYS Sowmya Indrakumar (Mon Dec 12 2016 - 12:14:03 PST)
- [AMBER] REMD with pressure coupling Neale, Christopher Andrew (Mon Dec 12 2016 - 12:44:24 PST)
- [AMBER] Problems during solvation of molecule from Protein Data Bank The Cromicus Productions (Mon Dec 12 2016 - 13:52:15 PST)
- [AMBER] MMPBSA Quasi-Harmonic Entropy Sachin Natesh (Mon Dec 12 2016 - 20:16:26 PST)
- [AMBER] Zinc Oxide and protein simulation with AMBER vivek m (Tue Dec 13 2016 - 01:35:19 PST)
- [AMBER] Minimum distance between imgaes A kS (Tue Dec 13 2016 - 05:39:07 PST)
- [AMBER] Re_Re: Editing residue in PDB file Nikolay N. Kuzmich (Tue Dec 13 2016 - 06:27:10 PST)
- [AMBER] The right character for logical AND in mask definition in MMPBSA ? Marek Maly (Tue Dec 13 2016 - 09:40:59 PST)
- [AMBER] Fwd: AmberTools 16: IBM XL Compiler Support James Ostrander (Tue Dec 13 2016 - 12:52:02 PST)
- [AMBER] Hydrogen bond calculataion richa anand (Tue Dec 13 2016 - 23:01:08 PST)
- [AMBER] mmpbsa snapshots Mary Varughese (Wed Dec 14 2016 - 00:18:31 PST)
- [AMBER] Frequencies in AMBER, obtaining the hessian Stregone (Wed Dec 14 2016 - 03:14:20 PST)
- [AMBER] Uridine diphosphate rhamnose (UDP-Rha) Imma Speciale (Wed Dec 14 2016 - 07:10:13 PST)
- [AMBER] sviol script error ? Benjamin Chagot (Wed Dec 14 2016 - 08:08:52 PST)
- [AMBER] cpptraj cluster -representative structure Thomas Pochapsky (Wed Dec 14 2016 - 08:13:54 PST)
- [AMBER] Constant pH across membrane Fabrício Bracht (Wed Dec 14 2016 - 15:49:34 PST)
- [AMBER] About Constant pH Molecular Dynamics 上海科技大学 吴萌 (Wed Dec 14 2016 - 17:49:50 PST)
- [AMBER] Two different graphics cards in the same PC for pmemd.cuda Anton Perera (Wed Dec 14 2016 - 20:09:28 PST)
- [AMBER] difference between %occupied and lifetime in hydrogen bond analysis Andrew Bostick (Thu Dec 15 2016 - 00:17:32 PST)
- [AMBER] pmemd.cuda incomplete output file Andreas Tosstorff (Thu Dec 15 2016 - 06:59:43 PST)
- [AMBER] Remove water from mdvel file The Cromicus Productions (Thu Dec 15 2016 - 13:25:16 PST)
- [AMBER] Specify Grid Origin in 3D-RISM - Is it possible? Lucia Fusani (Fri Dec 16 2016 - 06:45:16 PST)
- [AMBER] ensuring lack of non-equilibrium jolt on restart Neale, Christopher Andrew (Fri Dec 16 2016 - 10:30:02 PST)
- [AMBER] Unknown atom type EP A kS (Sat Dec 17 2016 - 03:53:09 PST)
- [AMBER] Constant pH Molecular Dynamics for membrane protein 上海科技大学 吴萌 (Sun Dec 18 2016 - 18:01:43 PST)
- [AMBER] TI calculation problem in pmemd cuiyinglukitty (Sun Dec 18 2016 - 22:34:12 PST)
- Re: [AMBER] Issue with the gaff parameters for "nh" atom type David Case (Mon Dec 19 2016 - 05:22:13 PST)
- [AMBER] parmchk2 multiple parameters Andreas Gavrielides (Mon Dec 19 2016 - 06:53:01 PST)
- [AMBER] Error in rst file Mohaddeseh Habibzadeh (Mon Dec 19 2016 - 07:54:53 PST)
- [AMBER] Amber16 on GPUs and speed differences between CUDA_VISIBLE_DEVICES=0, 1 or 0, 2 Neale, Christopher Andrew (Mon Dec 19 2016 - 10:09:00 PST)
- [AMBER] Amber16 on GPUs and speed differences between CUDA_VISIBLE_DEVICES=0, 1 or 0, 2 Neale, Christopher Andrew (Mon Dec 19 2016 - 10:31:19 PST)
- [AMBER] Amber16 on GPUs and speed differences between CUDA_VISIBLE_DEVICES=0, 1 or 0, 2 Neale, Christopher Andrew (Mon Dec 19 2016 - 11:22:21 PST)
- [AMBER] locating cpinutil.py file Tsibela German Tebello Mofokeng (Mon Dec 19 2016 - 11:29:00 PST)
- [AMBER] Benign typo for a constant in barostats.F90 Neale, Christopher Andrew (Mon Dec 19 2016 - 13:52:00 PST)
- [AMBER] ERROR no map function for HH12 ARG srinivas penumutchu (Mon Dec 19 2016 - 13:53:11 PST)
- [AMBER] Error: The system has extended beyond the extent of the virtual box. Taylor, Miles (Mon Dec 19 2016 - 19:11:00 PST)
- [AMBER] bad atom type MN2+ ions in the binding free energy decomposition (Amber14) 袁浩亮 (Tue Dec 20 2016 - 06:25:27 PST)
- [AMBER] How to have a certain number of water molecules? Azade Yazdan Yar (Tue Dec 20 2016 - 07:39:07 PST)
- [AMBER] problem building Amber 16 with Intel compilers Susan Chacko (Tue Dec 20 2016 - 08:42:19 PST)
- [AMBER] addion issue Hirdesh Kumar (Tue Dec 20 2016 - 10:15:58 PST)
- [AMBER] Problem building FEW and mmpbsa.pl in Amber16 Tong Zhu (Tue Dec 20 2016 - 19:13:00 PST)
- [AMBER] Possible conformations predicted by MD from NMR data (RDC, dihedral) Trang Nguyen (Tue Dec 20 2016 - 22:42:10 PST)
- [AMBER] rdf_with_center_in_cpptraj_16 JAIME RUBIO MARTINEZ (Wed Dec 21 2016 - 05:01:57 PST)
- [AMBER] Problem about one GPU & multiple CPUs 吴萌 (Wed Dec 21 2016 - 05:38:21 PST)
- [AMBER] cpptraj LIE on a ghost-atom Elisa Pieri (Wed Dec 21 2016 - 06:45:22 PST)
- [AMBER] Force field modifications Jonathan Huihui (Wed Dec 21 2016 - 11:48:58 PST)
- [AMBER] solvatebox command Mohaddeseh Habibzadeh (Thu Dec 22 2016 - 01:36:46 PST)
- [AMBER] How to perform energy decomposition in Thermodynamic integration with Sander in Amber 14? Stefan Ivanov (Thu Dec 22 2016 - 02:55:49 PST)
- [AMBER] neutralization and Salt concentration for DNA simulations Muthukumaran R (Thu Dec 22 2016 - 05:25:18 PST)
- [AMBER] error in amber 16 mpi installation Michael Shokhen (Thu Dec 22 2016 - 10:35:30 PST)
- [AMBER] Amber16 configure: error: could not find mpi library for --enable-mpi Michael Shokhen (Thu Dec 22 2016 - 12:07:34 PST)
- [AMBER] failed testing cuda Michael Shokhen (Sun Dec 25 2016 - 10:36:48 PST)
- [AMBER] Problem in not defining the hybridization of a atomtype A kS (Mon Dec 26 2016 - 07:37:16 PST)
- [AMBER] 2D distance plots Abhilash J (Mon Dec 26 2016 - 10:18:59 PST)
- [AMBER] SEP non-standard phosphoserine issue. Saman Yousuf ali (Mon Dec 26 2016 - 23:02:47 PST)
- [AMBER] Distance diffusion calculation in ptraj and cpptraj wei (Mon Dec 26 2016 - 23:58:46 PST)
- [AMBER] Water density near the protein suspiciously low I Lőrincz (Tue Dec 27 2016 - 13:54:53 PST)
- [AMBER] 回复：Re: Distance diffusion calculation in ptraj and cpptraj wei (Tue Dec 27 2016 - 18:07:51 PST)
- [AMBER] Proplem about how to set substrate concentration Shanghaitech University WuMeng (Tue Dec 27 2016 - 23:38:54 PST)
- [AMBER] cuda.h: No such file or directory Elka Firmanda (Wed Dec 28 2016 - 17:16:25 PST)
- [AMBER] help in restart file Robin Jain (Thu Dec 29 2016 - 22:14:33 PST)
- [AMBER] Should I image atoms when I calculate translational and rotational diffusion constants with cpptraj? wei (Thu Dec 29 2016 - 22:51:27 PST)
- [AMBER] Umbrella sampling (US) along RMSD-based coordinates using targeted MD script Tarsis (Fri Dec 30 2016 - 07:49:51 PST)
- [AMBER] Principal Component Analysis (PCA) query. Abhilash J (Fri Dec 30 2016 - 09:39:21 PST)
- [AMBER] Remove motion of center of mass after obtaining trajectory The Cromicus Productions (Fri Dec 30 2016 - 11:54:25 PST)
- Last message date: Sat Dec 31 2016 - 00:00:03 PST
- Archived on: Wed Dec 25 2024 - 05:55:27 PST
