Amber Archive Jul 2018: by author

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

Amber Archive Jul 2018 by author