Amber Archive Jul 2018: by subject

[AMBER] ACE_NME_TLEAP
- Antonio Carlesso (Thu Jul 19 2018 - 12:56:16 PDT)
- Bill Ross (Thu Jul 19 2018 - 10:32:16 PDT)
- Antonio Carlesso (Wed Jul 18 2018 - 23:38:43 PDT)
[AMBER] Advice on using GLYCAM parameters
- Lachele Foley (Tue Jul 24 2018 - 08:34:00 PDT)
- senal dinuka (Tue Jul 17 2018 - 23:51:08 PDT)
[AMBER] AMBER Digest, Vol 2349, Issue 1
- Daniel Roe (Fri Jul 20 2018 - 07:25:36 PDT)
- Stejskal, Lenka (Tue Jul 17 2018 - 07:46:17 PDT)
[AMBER] Amber ff for oniom method
- Hector A. Baldoni (Mon Jul 30 2018 - 05:09:43 PDT)
- roja rahmani (Mon Jul 30 2018 - 04:41:08 PDT)
- David A Case (Mon Jul 30 2018 - 04:18:47 PDT)
- Rinsha Chk (Sun Jul 29 2018 - 21:27:07 PDT)
- Rinsha Chk (Sun Jul 29 2018 - 21:26:36 PDT)
- roja rahmani (Sun Jul 29 2018 - 21:15:22 PDT)
[AMBER] Amber on GTX 1-5- / 1050 TI ?
- Gustavo Seabra (Wed Jul 18 2018 - 08:06:12 PDT)
[AMBER] Amber on GTX 1050 / 1050 TI
- Gustavo Seabra (Thu Jul 19 2018 - 04:17:22 PDT)
- Jinfeng Chen (Thu Jul 19 2018 - 04:08:03 PDT)
- Gustavo Seabra (Thu Jul 19 2018 - 02:26:35 PDT)
[AMBER] Amber targeted MD restraintmask
- Carlos Simmerling (Fri Jul 20 2018 - 05:00:20 PDT)
- 李耀 (Thu Jul 19 2018 - 19:57:33 PDT)
[AMBER] Amber targeted MD tgtmdfrc
- 李耀 (Sat Jul 28 2018 - 22:29:19 PDT)
- Carlos Simmerling (Sat Jul 28 2018 - 10:50:21 PDT)
- 李耀 (Sat Jul 28 2018 - 09:59:25 PDT)
[AMBER] Amber targeted MD variables
- Carlos Simmerling (Mon Jul 23 2018 - 03:42:07 PDT)
- 李耀 (Mon Jul 23 2018 - 02:57:44 PDT)
[AMBER] amber test run
- Bill Ross (Fri Jul 20 2018 - 06:23:19 PDT)
- ilhan.yavuz (Fri Jul 20 2018 - 05:59:53 PDT)
[AMBER] Amber16 to Amber18 upgrade?
- Pengfei Li (Thu Jul 12 2018 - 14:24:11 PDT)
- Hirdesh Kumar (Thu Jul 12 2018 - 13:46:13 PDT)
[AMBER] AMBER: QM/MM calculations using GPU
- Witkin, Katharine R (Tue Jul 03 2018 - 16:10:35 PDT)
- Goetz, Andreas (Tue Jul 03 2018 - 14:58:57 PDT)
- Witkin, Katharine R (Tue Jul 03 2018 - 13:07:50 PDT)
- Goetz, Andreas (Tue Jul 03 2018 - 13:05:01 PDT)
- Qinghua Liao (Tue Jul 03 2018 - 13:02:45 PDT)
- Witkin, Katharine R (Tue Jul 03 2018 - 12:52:07 PDT)
[AMBER] analyze force on selected atoms
- James Kress (Mon Jul 23 2018 - 12:22:20 PDT)
[AMBER] Arsenous acid (H3AsO3) parameterization
- Zuo, Zhicheng (Thu Jul 19 2018 - 21:25:32 PDT)
[AMBER] Au+++ ion parameter
- Aashish Bhatt (Tue Jul 17 2018 - 04:18:36 PDT)
[AMBER] Calcium force fields
- Qinghua Liao (Wed Jul 18 2018 - 09:29:47 PDT)
- Piotr Fajer (Wed Jul 18 2018 - 08:53:39 PDT)
- David A Case (Wed Jul 18 2018 - 04:16:10 PDT)
[AMBER] Calcium forcefields
- Zuo, Zhicheng (Wed Jul 18 2018 - 07:30:39 PDT)
- Aashish Bhatt (Tue Jul 17 2018 - 22:35:59 PDT)
- Piotr Fajer (Tue Jul 17 2018 - 10:36:55 PDT)
[AMBER] calculating headgroup ion-ion and ion-dipole contacts for lipid bilayers
- Wesley Michael Botello-Smith (Tue Jul 24 2018 - 12:06:54 PDT)
- Wesley Michael Botello-Smith (Tue Jul 24 2018 - 10:32:46 PDT)
- Sally Pias (Tue Jul 24 2018 - 10:16:58 PDT)
- Hai Nguyen (Fri Jul 20 2018 - 17:01:18 PDT)
- Wesley Michael Botello-Smith (Fri Jul 20 2018 - 16:56:51 PDT)
- Daniel Roe (Fri Jul 20 2018 - 08:03:41 PDT)
- Sally Pias (Fri Jul 13 2018 - 15:14:33 PDT)
[AMBER] Calcutaion of the observed acceptance ratio from simulation
- Daniel Roe (Fri Jul 06 2018 - 06:23:08 PDT)
- RITUPARNA ROY (Fri Jul 06 2018 - 06:07:46 PDT)
[AMBER] Cannot run pdb4amber
- Alen Ahmetovic (Thu Jul 12 2018 - 13:56:58 PDT)
- David A Case (Thu Jul 12 2018 - 05:48:08 PDT)
- Hai Nguyen (Wed Jul 11 2018 - 21:37:25 PDT)
- Alen Ahmetovic (Wed Jul 11 2018 - 21:27:24 PDT)
[AMBER] convert trajectories files in AMBER
- Charles-Alexandre Mattelaer (Fri Jul 13 2018 - 10:43:34 PDT)
- Chhaya Singh (Fri Jul 13 2018 - 10:31:00 PDT)
[AMBER] CPPTRAJ contacts and nativecontacts
- PAQUET Amaury (Tue Jul 31 2018 - 04:11:52 PDT)
- Daniel Roe (Fri Jul 27 2018 - 08:53:27 PDT)
- Wesley Michael Botello-Smith (Fri Jul 27 2018 - 08:47:45 PDT)
- Wesley Michael Botello-Smith (Fri Jul 27 2018 - 08:41:22 PDT)
- PAQUET Amaury (Fri Jul 27 2018 - 07:16:35 PDT)
[AMBER] Cpptraj PCA analysis - correlation between PCs?
- Markowska (Tue Jul 31 2018 - 06:22:35 PDT)
- Markowska (Tue Jul 31 2018 - 01:28:55 PDT)
[AMBER] CPPTRAJ read different frames
- Daniel Roe (Fri Jul 20 2018 - 07:01:23 PDT)
- Rana Rehan Khalid (Thu Jul 19 2018 - 15:45:01 PDT)
- Daniel Roe (Thu Jul 19 2018 - 10:40:09 PDT)
- Rana Rehan Khalid (Thu Jul 19 2018 - 10:08:23 PDT)
[AMBER] Cuda
- Zahra Khatti (Tue Jul 03 2018 - 08:14:20 PDT)
- Ross Walker (Mon Jul 02 2018 - 05:02:14 PDT)
[AMBER] CUDA and Amber 18
- David A Case (Mon Jul 16 2018 - 13:00:11 PDT)
- Darrin York (Mon Jul 16 2018 - 05:36:55 PDT)
- Beale, John (Mon Jul 16 2018 - 05:15:46 PDT)
[AMBER] Determination of pmf, diffuse, permeability and resistance in case of lipid molecule?
- zmatovic.kg.ac.rs (Tue Jul 17 2018 - 09:03:11 PDT)
- Dickson, Callum (Tue Jul 17 2018 - 07:47:22 PDT)
- zmatovic.kg.ac.rs (Mon Jul 16 2018 - 02:33:26 PDT)
[AMBER] Diffusion coefficient from Terachem
- emanuele falbo (Thu Jul 19 2018 - 07:52:43 PDT)
[AMBER] Distance between two different solvent mask
- MOHD HOMAIDUR RAHMAN (Sat Jul 21 2018 - 02:04:03 PDT)
- Daniel Roe (Fri Jul 20 2018 - 07:55:14 PDT)
- MOHD HOMAIDUR RAHMAN (Mon Jul 16 2018 - 03:23:53 PDT)
[AMBER] Distance restraint for PMEMD
- Abir Ganguly (Fri Jul 20 2018 - 07:18:23 PDT)
- Feng Pan (Thu Jul 19 2018 - 14:13:59 PDT)
- David A Case (Thu Jul 19 2018 - 12:38:47 PDT)
- Abir Ganguly (Thu Jul 19 2018 - 05:48:20 PDT)
[AMBER] distance restraints and accelerated MD
- Carlos Simmerling (Sun Jul 08 2018 - 17:14:33 PDT)
- giulia palermo (Sun Jul 08 2018 - 17:08:00 PDT)
[AMBER] eCheminfo Milano July 16-29, Training and Innovation Course in Drug Design 2018, bursary and early-bird deadline ending soon
- Thomas Exner (Mon Jul 02 2018 - 03:05:47 PDT)
[AMBER] eCheminfo Oxford 3-7 Sep., Training and Innovation Course in Drug Design, bursary and early-bird deadline approaching quickly
- Thomas Exner (Mon Jul 23 2018 - 05:53:12 PDT)
[AMBER] Energy file generation problem of pmemd.cuda
- David A Case (Sat Jul 07 2018 - 15:34:56 PDT)
- Meng Wu (Sat Jul 07 2018 - 06:02:17 PDT)
[AMBER] error in antechamber
- Bill Ross (Sat Jul 21 2018 - 13:27:26 PDT)
- Andrew Bostick (Sat Jul 21 2018 - 13:15:41 PDT)
[AMBER] error in leap prmtop incprd preparation
- Matias Machado (Sun Jul 15 2018 - 15:59:11 PDT)
- Bill Ross (Sun Jul 15 2018 - 13:37:16 PDT)
- senal dinuka (Sun Jul 15 2018 - 08:10:59 PDT)
[AMBER] Error in MCPB.py step 2
- Pengfei Li (Thu Jul 12 2018 - 14:22:43 PDT)
- dhaval patel (Thu Jul 12 2018 - 12:36:06 PDT)
[AMBER] Error while perform ALA Scanning Mutageneis
- Mitul Srivastava (Thu Jul 05 2018 - 00:42:41 PDT)
[AMBER] Error: an illegal memory access was encountered launching kernel kClearForces
- Kandes, Martin (Tue Jul 10 2018 - 23:37:37 PDT)
- David Cerutti (Tue Jul 10 2018 - 19:02:50 PDT)
- Kandes, Martin (Tue Jul 10 2018 - 16:46:35 PDT)
[AMBER] Extract Force from MDCRD/DCD trj
- James Kress (Fri Jul 27 2018 - 15:07:40 PDT)
- David A Case (Fri Jul 27 2018 - 05:21:12 PDT)
- Lod King (Thu Jul 26 2018 - 23:40:21 PDT)
- Hai Nguyen (Wed Jul 25 2018 - 20:33:47 PDT)
- Lod King (Wed Jul 25 2018 - 17:50:09 PDT)
[AMBER] Extraction of atomic charges.
- Jissy Akkarapattiakal Kuriappan (Mon Jul 02 2018 - 02:41:38 PDT)
- Vishal Kumar (Sun Jul 01 2018 - 05:32:44 PDT)
[AMBER] Fit the trajectory to the original inpcrd file
- Daniel Roe (Fri Jul 06 2018 - 06:26:51 PDT)
- Meng Wu (Fri Jul 06 2018 - 05:40:31 PDT)
[AMBER] FMNH2 parameters
- Maximilian Ebert (Tue Jul 31 2018 - 20:31:28 PDT)
[AMBER] Fwd: issues with accelerated MD in chloroform
- Chetna Tyagi (Fri Jul 13 2018 - 03:48:15 PDT)
[AMBER] Gaff vs Gaff2 when using antechamber to generate charges
- Yuliana Bosken (Mon Jul 30 2018 - 13:06:11 PDT)
- Junmei Wang (Mon Jul 30 2018 - 12:50:33 PDT)
- Yuliana Bosken (Mon Jul 30 2018 - 11:16:28 PDT)
- Yuliana Bosken (Sun Jul 29 2018 - 10:23:42 PDT)
- David A Case (Sun Jul 29 2018 - 05:13:16 PDT)
- Yuliana Bosken (Sun Jul 29 2018 - 04:44:41 PDT)
- Yuliana Bosken (Sat Jul 28 2018 - 15:31:48 PDT)
[AMBER] Geforce GTX 1080Ti testing on Amber18/CUDA 9.2
- Nikolay N. Kuzmich (Wed Jul 04 2018 - 12:15:00 PDT)
- Ross Walker (Mon Jul 02 2018 - 04:57:26 PDT)
[AMBER] global scaling of vdW
- David A Case (Thu Jul 05 2018 - 05:35:59 PDT)
- Korey M Reid (Tue Jul 03 2018 - 11:10:02 PDT)
[AMBER] H-REMD ligand binding
- Milo Westler (Wed Jul 11 2018 - 11:16:45 PDT)
[AMBER] Help on
- Wesley Michael Botello-Smith (Mon Jul 09 2018 - 10:46:23 PDT)
- Stephan Schott (Mon Jul 09 2018 - 10:32:21 PDT)
- Kenneth Huang (Mon Jul 09 2018 - 10:20:08 PDT)
- Elisa Pieri (Mon Jul 09 2018 - 06:12:07 PDT)
[AMBER] How should I perform a long-time Simulated Annealing MD?
- David A Case (Wed Jul 04 2018 - 19:06:11 PDT)
- Robert Molt (Wed Jul 04 2018 - 15:22:39 PDT)
- David A Case (Wed Jul 04 2018 - 05:41:42 PDT)
- xmgign.126.com (Tue Jul 03 2018 - 19:06:14 PDT)
- David A Case (Tue Jul 03 2018 - 15:53:27 PDT)
- xmgign.126.com (Tue Jul 03 2018 - 01:32:16 PDT)
[AMBER] How to analyse the PCA results?
- Markowska (Thu Jul 26 2018 - 06:41:40 PDT)
- Markowska (Thu Jul 26 2018 - 06:10:42 PDT)
- Daniel Roe (Fri Jul 20 2018 - 07:23:58 PDT)
- Daniel Roe (Fri Jul 20 2018 - 07:20:21 PDT)
- Markowska (Wed Jul 18 2018 - 09:01:59 PDT)
[AMBER] How to provide the CPIN input file argument for CpHMD in pmemd.cuda?
- Bharat Manna (Wed Jul 11 2018 - 05:49:59 PDT)
- Cruzeiro,Vinicius Wilian D (Tue Jul 10 2018 - 06:38:25 PDT)
- Bharat Manna (Mon Jul 09 2018 - 21:24:41 PDT)
- Eric Lang (Mon Jul 09 2018 - 04:58:23 PDT)
- Bharat Manna (Mon Jul 09 2018 - 03:31:39 PDT)
[AMBER] How to reference the integration algorithm?
- Elisa Pieri (Thu Jul 05 2018 - 05:44:24 PDT)
- David A Case (Thu Jul 05 2018 - 05:42:29 PDT)
- Elisa Pieri (Wed Jul 04 2018 - 10:31:42 PDT)
[AMBER] How to specify the protein position in box while using tleap
- David A Case (Tue Jul 03 2018 - 05:49:35 PDT)
- Bill Ross (Mon Jul 02 2018 - 18:58:11 PDT)
- Jinfeng Chen (Mon Jul 02 2018 - 18:15:25 PDT)
[AMBER] huge difference in GB and PB energies calculated with MMPBSA.py
- Wesley Michael Botello-Smith (Fri Jul 06 2018 - 12:17:40 PDT)
- Ray Luo (Fri Jul 06 2018 - 08:20:18 PDT)
- David A Case (Fri Jul 06 2018 - 05:29:57 PDT)
- Charles Mariasoosai (Fri Jul 06 2018 - 00:55:49 PDT)
[AMBER] implicit solvent remd simulation
- Chhaya Singh (Mon Jul 09 2018 - 09:37:55 PDT)
[AMBER] Individual bridging water lifetimes by closest?
- Daniel Roe (Tue Jul 03 2018 - 10:21:02 PDT)
- Kenneth Huang (Tue Jul 03 2018 - 10:16:30 PDT)
- Daniel Roe (Tue Jul 03 2018 - 05:38:45 PDT)
- Kenneth Huang (Mon Jul 02 2018 - 13:18:46 PDT)
- Daniel Roe (Mon Jul 02 2018 - 06:25:19 PDT)
[AMBER] Inquries about Non-periodic PMF profile
- Meng Wu (Mon Jul 30 2018 - 19:02:18 PDT)
- Feng Pan (Mon Jul 30 2018 - 12:06:30 PDT)
- Dickson, Callum (Mon Jul 30 2018 - 11:39:10 PDT)
- Meng Wu (Sun Jul 29 2018 - 18:54:15 PDT)
- Meng Wu (Sat Jul 28 2018 - 07:26:37 PDT)
[AMBER] Interpretation the result of pairwise per-residue MM/PB(GB)SA decomposition.
- walkingintheair (Wed Jul 04 2018 - 20:18:04 PDT)
[AMBER] Ionic strength in MM_PBSA
- David A Case (Wed Jul 11 2018 - 06:40:24 PDT)
- 龚乾坤 (Tue Jul 10 2018 - 19:39:35 PDT)
[AMBER] Is Amber18 compatible with GCC-7.x
- David A Case (Thu Jul 26 2018 - 07:00:58 PDT)
- Mirza Ahmed Hammad (Wed Jul 25 2018 - 20:15:27 PDT)
- Nikolay N. Kuzmich (Tue Jul 24 2018 - 14:41:19 PDT)
[AMBER] Is Amber18 compatible with GCC-7.x?
- David A Case (Tue Jul 24 2018 - 16:26:28 PDT)
- Ross Walker (Tue Jul 24 2018 - 08:19:53 PDT)
- David A Case (Tue Jul 24 2018 - 05:07:36 PDT)
- Mirza Ahmed Hammad (Mon Jul 23 2018 - 20:50:41 PDT)
- David A Case (Mon Jul 23 2018 - 07:55:58 PDT)
- Mirza Ahmed Hammad (Fri Jul 20 2018 - 23:59:29 PDT)
[AMBER] issues with accelerated MD in chloroform
- Chetna Tyagi (Mon Jul 09 2018 - 11:37:11 PDT)
[AMBER] Lipid NMR order parameters
- Christopher Faulkner (Thu Jul 12 2018 - 00:16:17 PDT)
- Daniel Roe (Tue Jul 10 2018 - 09:12:38 PDT)
- Christopher Faulkner (Tue Jul 10 2018 - 05:53:30 PDT)
[AMBER] LJEDIT syntax
- David Cerutti (Tue Jul 24 2018 - 17:05:22 PDT)
- Matias Machado (Tue Jul 24 2018 - 14:01:45 PDT)
- Matias Machado (Tue Jul 24 2018 - 13:58:15 PDT)
- David Cerutti (Mon Jul 23 2018 - 12:09:38 PDT)
- Matias Machado (Mon Jul 23 2018 - 11:15:50 PDT)
[AMBER] mask behavior with ions?
- Daniel Roe (Fri Jul 20 2018 - 07:06:55 PDT)
- Kenneth Huang (Wed Jul 18 2018 - 10:37:01 PDT)
[AMBER] MCBP force constants
- Pengfei Li (Thu Jul 26 2018 - 08:08:38 PDT)
- Seibold, Steve Allan (Wed Jul 25 2018 - 10:23:02 PDT)
[AMBER] MM_PBSA/GBSA
- 龚乾坤 (Tue Jul 10 2018 - 04:51:15 PDT)
[AMBER] Need help regarding Constant pH MD in pmemd.cuda
- Bharat Manna (Thu Jul 05 2018 - 23:37:08 PDT)
[AMBER] Need help regarding CpHMD with T-REMD
- Saikat Dutta chowdhury (Mon Jul 09 2018 - 07:58:42 PDT)
- Cruzeiro,Vinicius Wilian D (Fri Jul 06 2018 - 07:29:53 PDT)
- Saikat Dutta chowdhury (Fri Jul 06 2018 - 03:52:10 PDT)
[AMBER] Neural net timestep integration diagram
- Bill Ross (Tue Jul 17 2018 - 17:54:58 PDT)
[AMBER] packmol error
- Gould, Ian R (Thu Jul 05 2018 - 05:43:04 PDT)
- David A Case (Thu Jul 05 2018 - 05:37:37 PDT)
- Gustaf Olsson (Wed Jul 04 2018 - 00:29:32 PDT)
[AMBER] Papers that use RPMD in AMBER
- Rodrigo Pérez Cossio (Fri Jul 20 2018 - 06:08:16 PDT)
[AMBER] partial molar volume of hypothetical protein molecule without atomic charges
- Tyler Luchko (Lists) (Fri Jul 27 2018 - 09:33:27 PDT)
- Leena Aggarwal (Fri Jul 27 2018 - 07:05:37 PDT)
- David A Case (Fri Jul 27 2018 - 05:25:13 PDT)
- Leena Aggarwal (Sat Jul 21 2018 - 02:45:51 PDT)
[AMBER] PCA multiple trajectories for mutants and wild type
- Daniel Roe (Thu Jul 12 2018 - 15:12:52 PDT)
- Wesley Michael Botello-Smith (Wed Jul 11 2018 - 11:07:36 PDT)
- Stejskal, Lenka (Wed Jul 11 2018 - 04:48:26 PDT)
[AMBER] peptide bond restraints
- lucrecia bogado (Thu Jul 19 2018 - 15:50:14 PDT)
- David A Case (Thu Jul 19 2018 - 05:53:37 PDT)
- lucrecia bogado (Wed Jul 18 2018 - 14:40:25 PDT)
- Carlos Simmerling (Fri Jul 13 2018 - 11:30:54 PDT)
- lucrecia bogado (Fri Jul 13 2018 - 11:23:26 PDT)
- Carlos Simmerling (Thu Jul 12 2018 - 16:08:22 PDT)
- Wesley Michael Botello-Smith (Thu Jul 12 2018 - 15:32:58 PDT)
- lucrecia bogado (Thu Jul 12 2018 - 15:19:50 PDT)
[AMBER] Per-residue energy decomposition by MMPBSA.pl
- S (Fri Jul 13 2018 - 23:30:40 PDT)
- Syeda (Fri Jul 13 2018 - 09:51:05 PDT)
[AMBER] Ph.D. candidate position in biomolecular modeling or bioinformatics
- Jan Brezovsky (Wed Jul 04 2018 - 03:26:44 PDT)
[AMBER] pmemd.cuda.MPI
- Shirin Jamshidi (Tue Jul 03 2018 - 16:41:54 PDT)
[AMBER] Possible bug on addLJType command of Parmed
- Matias Machado (Fri Jul 27 2018 - 20:20:19 PDT)
[AMBER] premed.cuda.MPI
- Shirin Jamshidi (Tue Jul 03 2018 - 16:40:40 PDT)
[AMBER] Problem in chamber
- Jason Swails (Thu Jul 26 2018 - 10:26:12 PDT)
- Suzan Bose (Tue Jul 24 2018 - 21:10:45 PDT)
[AMBER] problem preparing n-terminus with tleap (?)
- Matias Machado (Tue Jul 24 2018 - 20:07:18 PDT)
- Julia Belk (Tue Jul 24 2018 - 18:32:26 PDT)
[AMBER] Problem with NaN and Asteriks
- Bill Ross (Sat Jul 21 2018 - 11:05:36 PDT)
- Jorge Curima (Sat Jul 21 2018 - 00:12:47 PDT)
- Bill Ross (Tue Jul 17 2018 - 15:27:26 PDT)
- Jorge Curima (Tue Jul 17 2018 - 14:25:44 PDT)
- Bill Ross (Tue Jul 17 2018 - 13:58:00 PDT)
- Jorge Curima (Tue Jul 17 2018 - 13:44:07 PDT)
- Bill Ross (Tue Jul 17 2018 - 12:24:37 PDT)
- Jorge Curima (Tue Jul 17 2018 - 11:59:01 PDT)
[AMBER] Puckering parameters for pyranose ring
- David A Case (Mon Jul 09 2018 - 05:41:59 PDT)
- Rajarshi Roy (Mon Jul 09 2018 - 03:47:43 PDT)
- Charles-Alexandre Mattelaer (Sun Jul 08 2018 - 22:52:25 PDT)
- Rajarshi Roy (Sun Jul 08 2018 - 22:40:34 PDT)
[AMBER] QM/MM link atoms
- Gustavo Seabra (Tue Jul 31 2018 - 05:12:16 PDT)
- emanuele falbo (Tue Jul 31 2018 - 04:09:10 PDT)
[AMBER] Query about Salt-Concentration (soltcon) for Constant pH MD
- Cruzeiro,Vinicius Wilian D (Tue Jul 03 2018 - 07:03:18 PDT)
- Bharat Manna (Sun Jul 01 2018 - 22:51:09 PDT)
[AMBER] Query regarding multiplication of LJ parameters by a constant in topology file using parmed
- Leena Aggarwal (Thu Jul 26 2018 - 21:31:10 PDT)
- Jason Swails (Thu Jul 26 2018 - 10:30:17 PDT)
- Leena Aggarwal (Tue Jul 24 2018 - 21:36:27 PDT)
- David A Case (Tue Jul 24 2018 - 16:28:52 PDT)
- Leena Aggarwal (Tue Jul 24 2018 - 06:06:56 PDT)
[AMBER] Question about equilibration of membrane protein MD
- Wesley Michael Botello-Smith (Mon Jul 09 2018 - 09:55:10 PDT)
- 鲍劲霄 (Mon Jul 09 2018 - 02:14:56 PDT)
[AMBER] Question about implicit solvation: DNA-linker conjugate
- Supriyo Bhattacharya (Wed Jul 25 2018 - 10:32:20 PDT)
- Matias Machado (Tue Jul 24 2018 - 07:43:10 PDT)
- Supriyo Bhattacharya (Mon Jul 23 2018 - 13:53:50 PDT)
- Supriyo Bhattacharya (Mon Jul 23 2018 - 13:44:32 PDT)
- Carlos Simmerling (Mon Jul 23 2018 - 11:11:26 PDT)
- Hai Nguyen (Mon Jul 23 2018 - 11:06:32 PDT)
- Supriyo Bhattacharya (Sun Jul 22 2018 - 11:30:07 PDT)
[AMBER] Reading grid data from standard datafile
- Daniel Roe (Fri Jul 27 2018 - 09:27:49 PDT)
- Daniel Roe (Wed Jul 25 2018 - 06:25:07 PDT)
- I Lőrincz (Wed Jul 25 2018 - 04:55:09 PDT)
[AMBER] Reduced GPU Performance
- Ross Walker (Fri Jul 13 2018 - 11:45:47 PDT)
- Matias Machado (Fri Jul 13 2018 - 04:44:15 PDT)
- Midhun K Madhu (Fri Jul 13 2018 - 03:40:54 PDT)
[AMBER] Regarding Force constants from Mopac
- David A Case (Thu Jul 12 2018 - 05:34:37 PDT)
- Devashish_Das (Wed Jul 11 2018 - 09:30:22 PDT)
[AMBER] Regarding installation problem in CUDA 9.2
- Matias Machado (Wed Jul 04 2018 - 07:01:22 PDT)
- Debasish Mandal (Wed Jul 04 2018 - 03:37:39 PDT)
[AMBER] Regarding simulation of Organometallic compounds
- dhaval patel (Sat Jul 07 2018 - 04:11:52 PDT)
[AMBER] Regarding the MPI error in parallel running of 3D-RISM
- PRITI ROY (Wed Jul 25 2018 - 22:13:13 PDT)
- David A Case (Mon Jul 23 2018 - 08:50:33 PDT)
- PRITI ROY (Mon Jul 23 2018 - 04:00:40 PDT)
- Tyler Luchko (Lists) (Fri Jul 06 2018 - 16:17:48 PDT)
- PRITI ROY (Thu Jul 05 2018 - 03:39:32 PDT)
- David A Case (Wed Jul 04 2018 - 18:47:44 PDT)
- PRITI ROY (Wed Jul 04 2018 - 12:52:43 PDT)
[AMBER] Replica Exchange with Solute Tempering implementation in AMBER14/16/18 on GPUs
- Alan Hicks (Thu Jul 12 2018 - 10:38:15 PDT)
[AMBER] RST file setting in SMD
- David A Case (Thu Jul 05 2018 - 15:31:22 PDT)
- Meng Wu (Thu Jul 05 2018 - 05:56:06 PDT)
[AMBER] Running a small minimization with amber 16 package
- Debarati DasGupta (Tue Jul 31 2018 - 14:51:56 PDT)
- David A Case (Tue Jul 31 2018 - 11:33:06 PDT)
- Debarati DasGupta (Tue Jul 31 2018 - 09:34:26 PDT)
[AMBER] SANDER BOMB in subroutine qm2_extern_get_qm_forces
- Goetz, Andreas (Mon Jul 30 2018 - 10:17:05 PDT)
- Devashish_Das (Mon Jul 30 2018 - 01:07:32 PDT)
[AMBER] setting ionic strength in leap
- Kris Feher (Thu Jul 12 2018 - 12:02:30 PDT)
- Kris Feher (Thu Jul 12 2018 - 11:52:39 PDT)
- George M. Giambasu (Fri Jul 06 2018 - 21:34:45 PDT)
- Thomas C Bishop (Fri Jul 06 2018 - 08:51:14 PDT)
- Kris Feher (Fri Jul 06 2018 - 06:32:28 PDT)
- Thomas Cheatham (Thu Jul 05 2018 - 16:44:04 PDT)
- Kris Feher (Thu Jul 05 2018 - 13:45:26 PDT)
[AMBER] Si bonded parameters GAFF compatible
- Alechania Misturini (Fri Jul 06 2018 - 11:17:23 PDT)
[AMBER] Single Point Calculation on trajectory
- Raimon Fabregat (Fri Jul 13 2018 - 06:12:50 PDT)
[AMBER] Soft-core alchemical transformation in TI
- Simon Kit Sang Chu (Sat Jul 28 2018 - 08:17:47 PDT)
- accuratefreeenergy.gmail.com (Wed Jul 25 2018 - 09:37:30 PDT)
- Simon Kit Sang Chu (Wed Jul 25 2018 - 01:21:36 PDT)
- Simon Kit Sang Chu (Wed Jul 25 2018 - 09:17:52 PDT)
- accuratefreeenergy.gmail.com (Wed Jul 25 2018 - 09:10:48 PDT)
- Simon Kit Sang Chu (Wed Jul 25 2018 - 01:58:32 PDT)
- accuratefreeenergy.gmail.com (Tue Jul 24 2018 - 05:49:47 PDT)
- Simon Kit Sang Chu (Mon Jul 23 2018 - 19:44:28 PDT)
- David Cerutti (Mon Jul 23 2018 - 09:57:24 PDT)
- Simon Kit Sang Chu (Mon Jul 23 2018 - 08:11:35 PDT)
[AMBER] Some Parameters In MM_PB/GBSA
- David A Case (Sat Jul 07 2018 - 04:35:04 PDT)
- 龚乾坤 (Sat Jul 07 2018 - 04:10:07 PDT)
[AMBER] The Calculate Formula of Ionic strength in MM_PBSA/GBSA
- Wesley Michael Botello-Smith (Mon Jul 09 2018 - 09:45:13 PDT)
- David A Case (Mon Jul 09 2018 - 05:44:53 PDT)
- 龚乾坤 (Mon Jul 09 2018 - 01:40:56 PDT)
[AMBER] The instructions of the .out file
- Thomas Cheatham (Fri Jul 27 2018 - 13:37:27 PDT)
- Zhonghua Xia (Fri Jul 27 2018 - 04:04:35 PDT)
- Zhonghua Xia (Fri Jul 27 2018 - 03:57:25 PDT)
- Zhonghua Xia (Fri Jul 27 2018 - 03:48:05 PDT)
[AMBER] The right syntax for creating the given mask using logical operators - Not all arguments handled
- Marek Maly (Sat Jul 28 2018 - 06:31:07 PDT)
- David A Case (Sat Jul 28 2018 - 06:06:44 PDT)
- Marek Maly (Sat Jul 28 2018 - 05:39:02 PDT)
- Daniel Roe (Fri Jul 27 2018 - 08:51:28 PDT)
- Marek Maly (Fri Jul 27 2018 - 06:18:27 PDT)
[AMBER] Thermodyncamic Integration (TI)
- emanuele falbo (Mon Jul 30 2018 - 01:37:53 PDT)
- David A Case (Fri Jul 27 2018 - 12:04:51 PDT)
- emanuele falbo (Fri Jul 27 2018 - 08:45:14 PDT)
[AMBER] TI calculations
- David A Case (Wed Jul 04 2018 - 05:47:19 PDT)
- emanuele (Wed Jul 04 2018 - 03:15:35 PDT)
[AMBER] TIP4P inputs and tests
- Brian Radak (Tue Jul 31 2018 - 07:13:04 PDT)
[AMBER] Tleap Impose Doesn't work for defining some angle/diedral
- Alechania Misturini (Tue Jul 03 2018 - 06:28:26 PDT)
- David A Case (Tue Jul 03 2018 - 06:00:40 PDT)
- Daniel Roe (Tue Jul 03 2018 - 05:43:46 PDT)
- Alechania Misturini (Tue Jul 03 2018 - 04:57:37 PDT)
[AMBER] trajout last x frames cpptraj
- Daniel Roe (Mon Jul 23 2018 - 10:34:57 PDT)
[AMBER] translational diffusion coefficient from MSD
- Daniel Roe (Fri Jul 20 2018 - 08:01:20 PDT)
- Kris Feher (Sun Jul 15 2018 - 15:04:33 PDT)
- Daniel Roe (Sat Jul 14 2018 - 09:42:23 PDT)
- Kris Feher (Thu Jul 12 2018 - 15:44:36 PDT)
[AMBER] Tutorial B1 problems
- David A Case (Wed Jul 04 2018 - 18:19:38 PDT)
- Jennifer L. Muzyka (Mon Jul 02 2018 - 08:46:58 PDT)
[AMBER] very slow implicit simulation on GPU!!!
- Supriyo Bhattacharya (Sat Jul 28 2018 - 09:53:12 PDT)
- Matias Machado (Sat Jul 28 2018 - 08:37:07 PDT)
- Matias Machado (Fri Jul 27 2018 - 23:17:56 PDT)
- Parviz Seifpanahi Shabane (Fri Jul 27 2018 - 16:16:13 PDT)
- Parviz Seifpanahi Shabane (Fri Jul 27 2018 - 16:13:09 PDT)
- Roitberg,Adrian E (Fri Jul 27 2018 - 16:12:13 PDT)
- Supriyo Bhattacharya (Fri Jul 27 2018 - 16:07:08 PDT)
- Parviz Seifpanahi Shabane (Fri Jul 27 2018 - 16:01:47 PDT)
- Bill Ross (Fri Jul 27 2018 - 14:10:42 PDT)
- Bill Ross (Fri Jul 27 2018 - 14:09:04 PDT)
- Supriyo Bhattacharya (Fri Jul 27 2018 - 14:05:42 PDT)
- David Cerutti (Fri Jul 27 2018 - 14:03:09 PDT)
- Parviz Seifpanahi Shabane (Fri Jul 27 2018 - 13:46:23 PDT)
- Bill Ross (Fri Jul 27 2018 - 13:34:56 PDT)
- Parviz Seifpanahi Shabane (Fri Jul 27 2018 - 13:15:26 PDT)
[AMBER] Xleap does not (?) loadoff lib files
- Sebastian Muraru (Wed Jul 11 2018 - 06:20:58 PDT)
- Matias Machado (Tue Jul 10 2018 - 08:01:14 PDT)
- Sebastian Muraru (Tue Jul 10 2018 - 06:46:33 PDT)

Amber Archive Jul 2018 by subject