Amber Archive May 2014 by author
787 messages
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Starting
Wed Apr 30 2014 - 09:30:03 PDT,
Ending
Sat May 31 2014 - 12:30:02 PDT
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ABEL Stephane 175950
Re: [AMBER] Parameters for FAD
(Thu May 01 2014 - 06:37:41 PDT)
adm
[AMBER] please let me unsubscribe of this
(Wed May 07 2014 - 23:31:28 PDT)
Adrian Roitberg
Re: [AMBER] MD at constant pH and high temperature
(Mon May 26 2014 - 07:18:31 PDT)
Re: [AMBER] Scaling of atomic mass of water molecules
(Tue May 13 2014 - 09:50:20 PDT)
[AMBER] Fwd: Re: Amber webminar
(Tue May 06 2014 - 11:55:07 PDT)
Re: [AMBER] PMF as a function of Q, fraction of native contacts
(Tue May 06 2014 - 06:59:29 PDT)
ahmed.sajid.stfc.ac.uk
Re: [AMBER] "cudaDeviceEnablePeerAccess all CUDA-capable devices are busy or unavailable"
(Thu May 08 2014 - 01:31:07 PDT)
Re: [AMBER] "cudaDeviceEnablePeerAccess all CUDA-capable devices are busy or unavailable"
(Thu May 08 2014 - 01:28:40 PDT)
Re: [AMBER] "cudaDeviceEnablePeerAccess all CUDA-capable devices are busy or unavailable"
(Wed May 07 2014 - 23:28:05 PDT)
[AMBER] "cudaDeviceEnablePeerAccess all CUDA-capable devices are busy or unavailable"
(Wed May 07 2014 - 02:46:13 PDT)
Ahmet yıldırım
Re: [AMBER] acpype on ambertools13
(Mon May 05 2014 - 03:14:20 PDT)
[AMBER] acpype on ambertools13
(Mon May 05 2014 - 01:08:22 PDT)
Alan
Re: [AMBER] acpype on ambertools13
(Mon May 05 2014 - 08:16:36 PDT)
Alessandro Contini
Re: [AMBER] NH4+
(Wed May 21 2014 - 01:19:19 PDT)
Re: [AMBER] NH4+
(Mon May 19 2014 - 06:29:00 PDT)
Re: [AMBER] NH4+
(Mon May 19 2014 - 05:54:24 PDT)
amin.imtech.res.in
Re: [AMBER] amber in namd
(Fri May 30 2014 - 09:52:04 PDT)
Re: [AMBER] Problem in loading leaprc.zinc
(Fri May 23 2014 - 06:55:55 PDT)
[AMBER] Problem in loading leaprc.zinc
(Thu May 22 2014 - 23:05:06 PDT)
Re: [AMBER] Parameters for FAD
(Thu May 01 2014 - 22:19:09 PDT)
Re: [AMBER] Parameters for FAD
(Thu May 01 2014 - 12:05:44 PDT)
[AMBER] Parameters for FAD
(Thu May 01 2014 - 06:26:59 PDT)
Amir Shahmoradi
[AMBER] MMPBSA & mmpbsa_py_nabnmode frequent crashes
(Tue May 06 2014 - 17:07:45 PDT)
Ander
[AMBER] creating quadruplex structure with NAB
(Thu May 08 2014 - 05:12:41 PDT)
Aronica, Pietro
Re: [AMBER] Alanine Scanning MMPBSA
(Wed May 28 2014 - 06:36:07 PDT)
Re: [AMBER] Alanine Scanning MMPBSA
(Tue May 20 2014 - 06:21:54 PDT)
Re: [AMBER] Alanine Scanning MMPBSA
(Tue May 13 2014 - 05:01:54 PDT)
Re: [AMBER] Alanine Scanning MMPBSA
(Tue May 13 2014 - 04:06:08 PDT)
Re: [AMBER] Alanine Scanning MMPBSA
(Fri May 09 2014 - 06:01:57 PDT)
Re: [AMBER] Alanine Scanning MMPBSA
(Fri May 09 2014 - 03:27:46 PDT)
Re: [AMBER] Alanine Scanning MMPBSA
(Thu May 08 2014 - 10:08:13 PDT)
Re: [AMBER] Alanine Scanning MMPBSA
(Thu May 08 2014 - 09:45:12 PDT)
[AMBER] Alanine Scanning MMPBSA
(Thu May 08 2014 - 08:56:28 PDT)
Arun Kumar Somavarapu
[AMBER] Extending MMPBSA
(Sat May 17 2014 - 04:50:44 PDT)
Arunima Shilpi
[AMBER] error in plot of interaction energy in xmgrace
(Sat May 31 2014 - 06:03:22 PDT)
[AMBER] print residue
(Wed May 28 2014 - 22:07:29 PDT)
[AMBER] print residue
(Tue May 27 2014 - 22:07:04 PDT)
[AMBER] Residue Pairing ih MMPBSA calculation
(Mon May 26 2014 - 20:52:57 PDT)
[AMBER] delta Ggas and Delta Gsolv
(Fri May 09 2014 - 06:31:29 PDT)
[AMBER] Siginificance of delta G
(Fri May 09 2014 - 06:09:27 PDT)
Asaminew Haile
Re: [AMBER] problem using pmemd.cuda with barostat=2 option
(Sat May 31 2014 - 09:01:30 PDT)
[AMBER] problem using pmemd.cuda with barostat=2 option
(Sat May 31 2014 - 08:10:50 PDT)
Re: [AMBER] SASA error
(Fri May 23 2014 - 08:19:03 PDT)
Re: [AMBER] SASA calculation
(Fri May 23 2014 - 06:18:42 PDT)
Re: [AMBER] softcore potential flag
(Thu May 08 2014 - 09:44:04 PDT)
Re: [AMBER] Analysis of minimization stage
(Thu May 08 2014 - 09:13:57 PDT)
[AMBER] softcore potential flag
(Thu May 08 2014 - 07:37:23 PDT)
ASFARINA AMIR HASSAN
[AMBER] Error: invalid argument launching kernel kNLGenerateSpatialHash
(Thu May 08 2014 - 01:31:27 PDT)
Ben Ahmady
Re: [AMBER] Help with ptraj RDF/ion coordination shells/number of ions within regions
(Mon May 19 2014 - 02:04:01 PDT)
Re: [AMBER] Help with ptraj RDF/ion coordination shells/number of ions within regions
(Sun May 18 2014 - 13:43:45 PDT)
Re: [AMBER] Help with ptraj RDF/ion coordination shells/number of ions within regions
(Fri May 16 2014 - 09:40:04 PDT)
Re: [AMBER] Help with ptraj RDF/ion coordination shells/number of ions within regions
(Fri May 16 2014 - 07:29:42 PDT)
Ben.Cossins.ucb.com
[AMBER] Error: Could not compile with NetCDF Fortran interface gfortran-4.7 and amber14
(Thu May 15 2014 - 04:22:44 PDT)
Benjamin D Madej
Re: [AMBER] cant run ntp=3 without csurften
(Tue May 20 2014 - 11:22:34 PDT)
Re: [AMBER] cant run ntp=3 without csurften
(Tue May 20 2014 - 11:15:21 PDT)
berin karaman
Re: [AMBER] acetylated lysine - OXT
(Fri May 16 2014 - 07:07:11 PDT)
Re: [AMBER] acetylated lysine - OXT
(Fri May 16 2014 - 05:39:00 PDT)
[AMBER] acetylated lysine - OXT
(Fri May 16 2014 - 01:00:48 PDT)
Bharatham, Nagakumar
Re: [AMBER] MD at constant pH and high temperature. .
(Mon May 26 2014 - 08:48:21 PDT)
Biao Ma
Re: [AMBER] get sqm Error when run antechamber
(Fri May 16 2014 - 00:38:46 PDT)
Re: [AMBER] get sqm Error when run antechamber
(Wed May 14 2014 - 19:36:16 PDT)
Re: [AMBER] get sqm Error when run antechamber
(Wed May 14 2014 - 07:24:41 PDT)
[AMBER] get sqm Error when run antechamber
(Mon May 12 2014 - 23:44:04 PDT)
Bill Miller III
Re: [AMBER] Extending MMPBSA
(Sat May 17 2014 - 05:01:18 PDT)
Re: [AMBER] MMPBSA
(Sat May 17 2014 - 04:11:43 PDT)
Re: [AMBER] Alanine Scanning MMPBSA
(Thu May 08 2014 - 09:50:33 PDT)
Re: [AMBER] Alanine Scanning MMPBSA
(Thu May 08 2014 - 09:12:22 PDT)
Re: [AMBER] number of frames in MMPBGBSA
(Tue May 06 2014 - 07:29:07 PDT)
Re: [AMBER] alanine scanning
(Sat May 03 2014 - 12:03:45 PDT)
Bill Ross
Re: [AMBER] Saturday
(Fri May 16 2014 - 13:08:11 PDT)
Re: [AMBER] SolvateBox command
(Thu May 15 2014 - 16:30:00 PDT)
Brent Krueger
Re: [AMBER] Modeling systems with non-standard residues
(Sun May 11 2014 - 05:35:29 PDT)
Brian Radak
Re: [AMBER] periodic box buffer zone
(Fri May 30 2014 - 08:52:19 PDT)
Re: [AMBER] rmsd of multiple trajectories with different topologies and sizes but same reference
(Tue May 27 2014 - 08:41:24 PDT)
[AMBER] rmsd of multiple trajectories with different topologies and sizes but same reference
(Tue May 27 2014 - 07:43:08 PDT)
Re: [AMBER] compiling iAPBS and sander.APBS?
(Tue May 27 2014 - 05:40:10 PDT)
Re: [AMBER] compiling iAPBS and sander.APBS?
(Sun May 25 2014 - 08:17:43 PDT)
[AMBER] compiling iAPBS and sander.APBS?
(Fri May 23 2014 - 13:54:06 PDT)
Re: [AMBER] Analysis of minimization stage
(Tue May 20 2014 - 06:51:37 PDT)
Re: [AMBER] Help with ptraj RDF/ion coordination shells/number of ions within regions
(Fri May 16 2014 - 10:53:56 PDT)
Re: [AMBER] Help with ptraj RDF/ion coordination shells/number of ions within regions
(Fri May 16 2014 - 07:45:58 PDT)
Re: [AMBER] Scaling of atomic mass of water molecules
(Tue May 13 2014 - 08:21:58 PDT)
Re: [AMBER] Scaling of atomic mass of water molecules
(Tue May 13 2014 - 07:59:59 PDT)
Re: [AMBER] multinode NPT runs on GPU
(Fri May 09 2014 - 09:04:14 PDT)
Re: [AMBER] softcore potential flag
(Thu May 08 2014 - 10:17:58 PDT)
Re: [AMBER] PMF as a function of Q, fraction of native contacts
(Tue May 06 2014 - 06:51:02 PDT)
Carlos Simmerling
Re: [AMBER] Scaling of atomic mass of water molecules
(Tue May 13 2014 - 08:31:26 PDT)
Re: [AMBER] FapydG parameters
(Wed May 07 2014 - 06:54:04 PDT)
Re: [AMBER] PMF as a function of Q, fraction of native contacts
(Mon May 05 2014 - 16:25:58 PDT)
Christina Bergonzo
Re: [AMBER] Accelerated MD in Amber
(Wed May 28 2014 - 11:48:06 PDT)
Re: [AMBER] FapydG parameters
(Wed May 07 2014 - 06:51:25 PDT)
CHRISTOPHER PATRICK MCNARY
[AMBER] Antechamber
(Mon May 19 2014 - 08:18:03 PDT)
Cuiyl
Re: [AMBER] How to define the direction of the force in SMD method?
(Mon May 26 2014 - 23:10:08 PDT)
[AMBER] How to define the direction of the force in SMD method?
(Sun May 25 2014 - 19:14:08 PDT)
Daniel Hollas
[AMBER] sander QM/MM with terachem using MPI
(Sat May 31 2014 - 08:21:42 PDT)
Daniel Roe
Re: [AMBER] Accelerated MD in Amber
(Wed May 28 2014 - 06:57:56 PDT)
Re: [AMBER] PCA and the corresponding pdb
(Wed May 28 2014 - 06:37:39 PDT)
Re: [AMBER] PCA and the corresponding pdb
(Tue May 27 2014 - 13:39:36 PDT)
Re: [AMBER] rmsd of multiple trajectories with different topologies and sizes but same reference
(Tue May 27 2014 - 08:20:55 PDT)
Re: [AMBER] PCA and the corresponding pdb
(Tue May 27 2014 - 06:49:39 PDT)
Re: [AMBER] MD at pH5 and 50-55 degree celcius
(Tue May 27 2014 - 06:42:11 PDT)
Re: [AMBER] Accelerated MD in Amber
(Tue May 27 2014 - 06:39:32 PDT)
Re: [AMBER] Trajectory analysis using pptraj
(Tue May 27 2014 - 06:37:18 PDT)
Re: [AMBER] Interactions across the periodic box boundaries
(Wed May 21 2014 - 14:00:48 PDT)
Re: [AMBER] Temperature rises to 4000K during NVT equilibration
(Wed May 21 2014 - 11:51:13 PDT)
Re: [AMBER] Temperature rises to 4000K during NVT equilibration
(Wed May 21 2014 - 07:14:07 PDT)
Re: [AMBER] Temperature rises to 4000K during NVT equilibration
(Wed May 21 2014 - 07:03:19 PDT)
Re: [AMBER] Peptides moving out of the water box
(Wed May 21 2014 - 07:01:20 PDT)
Re: [AMBER] secondary structure calculation using Cpptraj
(Tue May 20 2014 - 13:45:41 PDT)
Re: [AMBER] Error in setting irest=1
(Tue May 20 2014 - 09:39:29 PDT)
Re: [AMBER] Trajectory analysis using pptraj
(Tue May 20 2014 - 08:57:29 PDT)
Re: [AMBER] Problem in parallel version of pmemd.cuda
(Tue May 20 2014 - 07:23:47 PDT)
Re: [AMBER] handling long trajs for PCA and components plot
(Mon May 19 2014 - 09:33:03 PDT)
Re: [AMBER] How to plot Eigenvectors against % Positional Fluctuations
(Mon May 19 2014 - 07:24:14 PDT)
Re: [AMBER] Script for Calculating RMSIP
(Mon May 19 2014 - 07:10:35 PDT)
Re: [AMBER] pairwise option in cpptraj
(Thu May 15 2014 - 14:06:58 PDT)
Re: [AMBER] torsion restraints not defined properly?
(Thu May 15 2014 - 13:43:40 PDT)
Re: [AMBER] pairwise option in cpptraj
(Thu May 15 2014 - 11:15:09 PDT)
Re: [AMBER] torsion restraints not defined properly?
(Thu May 15 2014 - 11:05:53 PDT)
Re: [AMBER] Analysis of minimization stage
(Thu May 15 2014 - 08:35:17 PDT)
Re: [AMBER] sander and processor
(Thu May 15 2014 - 08:27:14 PDT)
Re: [AMBER] when nastruct does NOT print the basepair information
(Thu May 15 2014 - 08:25:38 PDT)
Re: [AMBER] Error: Could not compile with NetCDF Fortran interface gfortran-4.7 and amber14
(Thu May 15 2014 - 08:19:30 PDT)
Re: [AMBER] about GPU memory requirements
(Wed May 14 2014 - 10:21:01 PDT)
Re: [AMBER] QM/MM tutorial
(Wed May 14 2014 - 09:42:56 PDT)
Re: [AMBER] get sqm Error when run antechamber
(Tue May 13 2014 - 10:36:37 PDT)
Re: [AMBER] Analysis of minimization stage
(Tue May 13 2014 - 08:58:07 PDT)
Re: [AMBER] Analysis of minimization stage
(Mon May 12 2014 - 11:00:40 PDT)
Re: [AMBER] handling long trajs for PCA and components plot
(Mon May 12 2014 - 10:28:25 PDT)
Re: [AMBER] Analysis of minimization stage
(Fri May 09 2014 - 07:04:58 PDT)
Re: [AMBER] Analysis of minimization stage
(Thu May 08 2014 - 10:10:02 PDT)
Re: [AMBER] Analysis of minimization stage
(Thu May 08 2014 - 09:21:40 PDT)
Re: [AMBER] handling long trajs for PCA and components plot
(Thu May 08 2014 - 08:04:14 PDT)
Re: [AMBER] handling long trajs for PCA and components plot
(Wed May 07 2014 - 07:52:12 PDT)
Re: [AMBER] re-imaging bilayer
(Wed May 07 2014 - 07:45:45 PDT)
Re: [AMBER] Processing a subset of mdcrd frames
(Tue May 06 2014 - 20:29:20 PDT)
Re: [AMBER] handling long trajs for PCA and components plot
(Tue May 06 2014 - 20:27:07 PDT)
Re: [AMBER] Processing a subset of mdcrd frames
(Tue May 06 2014 - 13:54:15 PDT)
Re: [AMBER] handling long trajs for PCA and components plot
(Tue May 06 2014 - 10:24:53 PDT)
Re: [AMBER] Extract MD co-ordinates
(Mon May 05 2014 - 09:27:24 PDT)
Re: [AMBER] Percent Occupancey with PCA
(Sat May 03 2014 - 00:11:50 PDT)
Re: [AMBER] Problems with the Amber-14 compilation with CUDA-5.5
(Thu May 01 2014 - 07:15:39 PDT)
David A Case
Re: [AMBER] Contributing new water models
(Wed May 28 2014 - 18:28:41 PDT)
Re: [AMBER] Disulfide Bond Info and XMIN Stuck Problems
(Wed May 28 2014 - 16:55:31 PDT)
Re: [AMBER] Disulfide Bond Info and XMIN Stuck Problems
(Wed May 28 2014 - 06:39:00 PDT)
Re: [AMBER] Disulfide Bond Info and XMIN Stuck Problems
(Tue May 27 2014 - 17:25:07 PDT)
Re: [AMBER] MD at constant pH and high temperature
(Mon May 26 2014 - 06:58:36 PDT)
Re: [AMBER] Attempting to modify Amber
(Thu May 22 2014 - 07:24:00 PDT)
Re: [AMBER] Temperature rises to 4000K during NVT equilibration
(Wed May 21 2014 - 07:29:57 PDT)
Re: [AMBER] sqm convergence failure
(Tue May 20 2014 - 08:30:20 PDT)
Re: [AMBER] Problem in parallel version of pmemd.cuda
(Mon May 19 2014 - 13:58:45 PDT)
Re: [AMBER] About the reproducibility of pmemd
(Mon May 19 2014 - 05:50:13 PDT)
Re: [AMBER] can “NAB: Molecular mechanics and dynamics” do qmmm caculation?
(Mon May 19 2014 - 04:51:22 PDT)
Re: [AMBER] antechamber with Au atom
(Mon May 19 2014 - 04:50:41 PDT)
Re: [AMBER] error in minimization
(Mon May 19 2014 - 04:48:54 PDT)
Re: [AMBER] error in minimization
(Sat May 17 2014 - 12:50:32 PDT)
Re: [AMBER] Analysis of minimization stage
(Fri May 16 2014 - 17:46:14 PDT)
Re: [AMBER] Analysis of minimization stage
(Fri May 16 2014 - 05:26:34 PDT)
Re: [AMBER] acetylated lysine - OXT
(Fri May 16 2014 - 05:19:49 PDT)
Re: [AMBER] torsion restraints not defined properly?
(Thu May 15 2014 - 12:12:52 PDT)
Re: [AMBER] get sqm Error when run antechamber
(Thu May 15 2014 - 04:52:00 PDT)
Re: [AMBER] Protocol for multiple CPU+ single GPU run on a single node,
(Wed May 14 2014 - 13:13:19 PDT)
Re: [AMBER] Analysis of minimization stage
(Wed May 14 2014 - 08:01:13 PDT)
Re: [AMBER] Need help as a beginner
(Tue May 13 2014 - 13:28:33 PDT)
Re: [AMBER] Analysis of minimization stage
(Mon May 12 2014 - 06:59:47 PDT)
Re: [AMBER] sqm convergence failure
(Mon May 12 2014 - 05:01:22 PDT)
Re: [AMBER] Force field of antechamber , parm94 ? parm99?
(Mon May 12 2014 - 04:52:04 PDT)
Re: [AMBER] problem with nmode
(Mon May 12 2014 - 04:49:44 PDT)
Re: [AMBER] Analysis of minimization stage
(Mon May 12 2014 - 04:47:04 PDT)
Re: [AMBER] Additional random motion of com for unwrapped trajectory
(Sun May 11 2014 - 06:00:34 PDT)
Re: [AMBER] Amber12 parallel installation error with MPICH2 UBUNTU 14.04
(Sat May 10 2014 - 14:58:43 PDT)
Re: [AMBER] Amber12 parallel installation error with MPICH2 UBUNTU 14.04
(Sat May 10 2014 - 05:30:40 PDT)
Re: [AMBER] sqm convergence failure
(Fri May 09 2014 - 12:49:27 PDT)
Re: [AMBER] Error when using PB implicit solvent in XMIN in NAB(PB Bomb in pb_init(): Allocation aborted)
(Fri May 09 2014 - 12:47:10 PDT)
Re: [AMBER] softcore potential flag
(Thu May 08 2014 - 09:32:33 PDT)
Re: [AMBER] syntax error and nab2c failed when using NAB
(Thu May 08 2014 - 05:59:21 PDT)
Re: [AMBER] Question about structure factor?
(Wed May 07 2014 - 15:18:20 PDT)
Re: [AMBER] Amber12 parallel installation error with MPICH2 UBUNTU 14.04
(Wed May 07 2014 - 05:32:25 PDT)
Re: [AMBER] PDB for 1-octanol molecules
(Wed May 07 2014 - 05:17:09 PDT)
Re: [AMBER] how to generate a complete amino acid in suitable for the vacuum simulation
(Wed May 07 2014 - 05:13:18 PDT)
Re: [AMBER] handling long trajs for PCA and components plot
(Mon May 05 2014 - 18:26:09 PDT)
Re: [AMBER] sander?
(Sun May 04 2014 - 08:27:33 PDT)
Re: [AMBER] Questions about nmode Command
(Sun May 04 2014 - 08:25:22 PDT)
Re: [AMBER] vlimit exceeded error when switch from NPT to NVE
(Sun May 04 2014 - 04:46:46 PDT)
Re: [AMBER] Problems with the Amber-14 compilation with CUDA-5.5
(Thu May 01 2014 - 06:54:42 PDT)
Re: [AMBER] Problems with the Amber-14 compilation with CUDA-5.5
(Thu May 01 2014 - 05:52:15 PDT)
David Chen
[AMBER] valve of VDW too high
(Thu May 08 2014 - 04:28:25 PDT)
Dongshan Wei
Re: [AMBER] syntax error and nab2c failed when using NAB
(Thu May 08 2014 - 06:27:15 PDT)
Re: [AMBER] syntax error and nab2c failed when using NAB
(Thu May 08 2014 - 06:05:30 PDT)
Re: [AMBER] syntax error and nab2c failed when using NAB
(Thu May 08 2014 - 05:36:37 PDT)
Re: [AMBER] syntax error and nab2c failed when using NAB
(Thu May 08 2014 - 05:14:00 PDT)
[AMBER] syntax error and nab2c failed when using NAB
(Thu May 08 2014 - 02:23:18 PDT)
Dropbox
[AMBER] Abdullahi Abubakar invited you to check out Dropbox
(Sun May 18 2014 - 18:58:02 PDT)
Duggan, Brendan
Re: [AMBER] torsion restraints not defined properly?
(Tue May 20 2014 - 11:55:30 PDT)
Re: [AMBER] AMBER Digest, Vol 855, Issue 1
(Thu May 15 2014 - 12:18:17 PDT)
[AMBER] torsion restraints not defined properly?
(Thu May 15 2014 - 10:55:29 PDT)
Eric Hill
Re: [AMBER] cant run ntp=3 without csurften
(Tue May 20 2014 - 12:56:29 PDT)
Re: [AMBER] cant run ntp=3 without csurften
(Tue May 20 2014 - 11:40:25 PDT)
[AMBER] cant run ntp=3 without csurften
(Tue May 20 2014 - 09:48:46 PDT)
[AMBER] csurften requirement for semiisotropic coupling
(Tue May 20 2014 - 09:34:42 PDT)
Eugene Yedvabny
[AMBER] Interactions across the periodic box boundaries
(Wed May 21 2014 - 12:19:40 PDT)
Re: [AMBER] Processing a subset of mdcrd frames
(Tue May 06 2014 - 15:19:21 PDT)
[AMBER] Processing a subset of mdcrd frames
(Tue May 06 2014 - 13:34:19 PDT)
Fabian Glaser
Re: [AMBER] AmberTools 14 compilation on OSX fails
(Thu May 15 2014 - 06:58:04 PDT)
Re: [AMBER] AmberTools 14 compilation on OSX fails
(Thu May 15 2014 - 05:50:01 PDT)
Re: [AMBER] AmberTools 14 compilation on OSX fails
(Thu May 15 2014 - 05:44:34 PDT)
Re: [AMBER] AmberTools 14 compilation on OSX fails
(Wed May 14 2014 - 22:42:11 PDT)
Re: [AMBER] AmberTools 14 compilation on OSX fails
(Wed May 14 2014 - 06:44:44 PDT)
[AMBER] AmberTools 14 compilation on OSX fails
(Wed May 14 2014 - 01:48:08 PDT)
fabien.ibanez.modis.fr.netgrs.com
Re: [AMBER] Installation AmberTools13
(Thu May 15 2014 - 01:24:13 PDT)
[AMBER] Installation AmberTools13
(Tue May 13 2014 - 07:30:53 PDT)
[AMBER] Installation of AmberTools13
(Mon May 05 2014 - 08:11:56 PDT)
Faez Iqbal khan
[AMBER] Urgent: unable to generate files
(Tue May 13 2014 - 01:20:43 PDT)
Fengxue Li
[AMBER] problem with nmode
(Mon May 12 2014 - 01:54:07 PDT)
[AMBER] AMBER : mmpbsa rms in nmode
(Sat May 10 2014 - 05:54:29 PDT)
[AMBER] mmpbsa: the nmode calculation
(Thu May 08 2014 - 23:11:07 PDT)
[AMBER] mmpbsa: the nmode calculation
(Thu May 08 2014 - 06:41:53 PDT)
FyD
Re: [AMBER] Parametrization of non-standart residues
(Sat May 31 2014 - 06:54:48 PDT)
Re: [AMBER] Parametrization of non-standart residues
(Sat May 31 2014 - 01:11:00 PDT)
Re: [AMBER] how to protonate phosphate groups of nucleotides
(Thu May 29 2014 - 00:08:35 PDT)
Re: [AMBER] zinc partial charges
(Wed May 28 2014 - 23:57:42 PDT)
Re: [AMBER] sqm convergence failure
(Tue May 20 2014 - 13:30:38 PDT)
Re: [AMBER] NH4+
(Mon May 19 2014 - 09:59:40 PDT)
Re: [AMBER] antechamber with Au atom
(Mon May 19 2014 - 10:02:53 PDT)
Re: [AMBER] sqm convergence failure
(Thu May 08 2014 - 04:23:27 PDT)
Re: [AMBER] Modeling systems with non-standard residues
(Thu May 08 2014 - 04:08:52 PDT)
Re: [AMBER] Prepareing branched residue
(Wed May 07 2014 - 12:05:34 PDT)
Re: [AMBER] Empirical force fields: release new version of RED Server Dev/PyRED
(Wed May 07 2014 - 11:38:09 PDT)
[AMBER] Fwd: Re: PDB for 1-octanol molecules
(Wed May 07 2014 - 08:16:17 PDT)
Re: [AMBER] PDB for 1-octanol molecules
(Wed May 07 2014 - 08:13:05 PDT)
Re: [AMBER] Empirical force fields: release new version of RED Server Dev/PyRED
(Wed May 07 2014 - 08:05:26 PDT)
Re: [AMBER] how to generate a complete amino acid in suitable for the vacuum simulation
(Wed May 07 2014 - 08:10:38 PDT)
Re: [AMBER] Empirical force fields: release new version of RED Server Dev/PyRED
(Mon May 05 2014 - 23:22:33 PDT)
[AMBER] Empirical force fields: release new version of RED Server Dev/PyRED
(Mon May 05 2014 - 04:00:11 PDT)
Re: [AMBER] Prepareing branched residue
(Sun May 04 2014 - 23:47:14 PDT)
Re: [AMBER] how to protonate phosphate groups of nucleotides
(Sun May 04 2014 - 22:19:14 PDT)
[AMBER] Fwd: Re: [q4md-fft] FAD parameters from F-90
(Sun May 04 2014 - 22:02:54 PDT)
George Patargias
Re: [AMBER] SolvateBox command
(Thu May 08 2014 - 08:13:35 PDT)
[AMBER] SolvateBox command
(Thu May 08 2014 - 03:50:34 PDT)
George Tzotzos
[AMBER] pmemd.MPI failure
(Fri May 09 2014 - 10:59:53 PDT)
Gerald Monard
Re: [AMBER] sqm convergence failure
(Tue May 20 2014 - 07:57:04 PDT)
giulia palermo
Re: [AMBER] conversion force constant
(Wed May 21 2014 - 01:32:15 PDT)
[AMBER] conversion force constant
(Mon May 19 2014 - 12:26:04 PDT)
[AMBER] antechamber with Au atom
(Mon May 19 2014 - 00:24:50 PDT)
Guqin Shi
Re: [AMBER] Disulfide Bond Info and XMIN Stuck Problems
(Thu May 29 2014 - 07:25:08 PDT)
Re: [AMBER] Disulfide Bond Info and XMIN Stuck Problems
(Wed May 28 2014 - 14:05:21 PDT)
Re: [AMBER] Disulfide Bond Info and XMIN Stuck Problems
(Tue May 27 2014 - 19:34:59 PDT)
[AMBER] Disulfide Bond Info and XMIN Stuck Problems
(Tue May 27 2014 - 09:14:29 PDT)
Re: [AMBER] Error when using PB implicit solvent in XMIN in NAB(PB Bomb in pb_init(): Allocation aborted)
(Fri May 09 2014 - 13:42:58 PDT)
Re: [AMBER] Error when using PB implicit solvent in XMIN in NAB(PB Bomb in pb_init(): Allocation aborted)
(Fri May 09 2014 - 13:35:50 PDT)
[AMBER] Error when using PB implicit solvent in XMIN in NAB(PB Bomb in pb_init(): Allocation aborted)
(Fri May 09 2014 - 11:44:03 PDT)
Gustavo Seabra
Re: [AMBER] "cudaDeviceEnablePeerAccess all CUDA-capable devices are busy or unavailable"
(Thu May 08 2014 - 06:10:58 PDT)
Hallel Freedman
Re: [AMBER] MMPBSA
(Thu May 29 2014 - 16:59:53 PDT)
Re: [AMBER] MMPBSA
(Thu May 29 2014 - 15:22:03 PDT)
Re: [AMBER] MMPBSA
(Thu May 29 2014 - 12:28:07 PDT)
Re: [AMBER] MMPBSA
(Thu May 29 2014 - 11:34:28 PDT)
Re: [AMBER] MMPBSA
(Wed May 28 2014 - 19:33:00 PDT)
Re: [AMBER] MMPBSA
(Wed May 28 2014 - 16:23:25 PDT)
Re: [AMBER] MMPBSA
(Wed May 28 2014 - 11:54:19 PDT)
Re: [AMBER] MMPBSA
(Wed May 28 2014 - 11:13:17 PDT)
[AMBER] MMPBSA
(Tue May 27 2014 - 11:05:32 PDT)
Hannes Loeffler
[AMBER] parmchk2 segfaults
(Fri May 16 2014 - 06:50:54 PDT)
Re: [AMBER] sqm convergence failure
(Mon May 12 2014 - 02:54:48 PDT)
Re: [AMBER] sqm convergence failure
(Thu May 08 2014 - 05:49:09 PDT)
Re: [AMBER] sqm convergence failure
(Thu May 08 2014 - 05:03:56 PDT)
[AMBER] sqm convergence failure
(Thu May 08 2014 - 03:16:06 PDT)
hannes.loeffler.stfc.ac.uk
Re: [AMBER] sqm convergence failure
(Thu May 08 2014 - 10:44:41 PDT)
Hector A. Baldoni
Re: [AMBER] Low energy path
(Wed May 21 2014 - 15:22:10 PDT)
[AMBER] Low energy path
(Wed May 21 2014 - 05:40:27 PDT)
Re: [AMBER] Script for Calculating RMSIP
(Sat May 17 2014 - 16:31:52 PDT)
Re: [AMBER] Recompile amber12 whit cuda 6.0
(Mon May 12 2014 - 12:46:15 PDT)
[AMBER] Recompile amber12 whit cuda 6.0
(Mon May 12 2014 - 12:00:36 PDT)
Ibrahim Said
Re: [AMBER] PCA and the corresponding pdb
(Tue May 27 2014 - 13:32:12 PDT)
[AMBER] PCA and the corresponding pdb
(Mon May 26 2014 - 11:54:38 PDT)
[AMBER] Analysis of evecs.dat file
(Fri May 09 2014 - 09:58:22 PDT)
Ilias Patmanidis
[AMBER] Peptides moving out of the water box
(Wed May 21 2014 - 06:47:39 PDT)
Ilyas Yildirim
Re: [AMBER] Need help as a beginner
(Tue May 13 2014 - 13:48:59 PDT)
Re: [AMBER] Need help as a beginner
(Tue May 13 2014 - 12:46:24 PDT)
Indrajit Deb
Re: [AMBER] Temperature rises to 4000K during NVT equilibration
(Wed May 21 2014 - 11:14:20 PDT)
Re: [AMBER] Temperature rises to 4000K during NVT equilibration
(Wed May 21 2014 - 07:56:35 PDT)
Re: [AMBER] Temperature rises to 4000K during NVT equilibration
(Wed May 21 2014 - 07:07:51 PDT)
[AMBER] Temperature rises to 4000K during NVT equilibration
(Wed May 21 2014 - 06:55:46 PDT)
James Maier
Re: [AMBER] Low energy path
(Wed May 21 2014 - 07:07:22 PDT)
Re: [AMBER] conversion force constant
(Mon May 19 2014 - 12:44:22 PDT)
Re: [AMBER] Protocol for multiple CPU+ single GPU run on a single node,
(Wed May 14 2014 - 12:30:08 PDT)
Re: [AMBER] pmemd.MPI failure
(Fri May 09 2014 - 11:18:28 PDT)
James Starlight
Re: [AMBER] Parametrization of non-standart residues
(Sat May 31 2014 - 06:21:30 PDT)
Re: [AMBER] Parametrization of non-standart residues
(Sat May 31 2014 - 04:50:56 PDT)
Re: [AMBER] Parametrization of non-standart residues
(Fri May 30 2014 - 23:07:39 PDT)
Re: [AMBER] Parametrization of non-standart residues
(Fri May 30 2014 - 12:04:01 PDT)
Re: [AMBER] Parametrization of non-standart residues
(Fri May 30 2014 - 12:00:14 PDT)
[AMBER] Parametrization of non-standart residues
(Fri May 30 2014 - 11:12:33 PDT)
Re: [AMBER] Accelerated MD in Amber
(Wed May 28 2014 - 10:37:38 PDT)
Re: [AMBER] Loop refirement
(Wed May 28 2014 - 00:29:44 PDT)
Re: [AMBER] Accelerated MD in Amber
(Wed May 28 2014 - 00:18:09 PDT)
[AMBER] Loop refirement
(Mon May 26 2014 - 03:06:13 PDT)
[AMBER] Accelerated MD in Amber
(Sun May 25 2014 - 06:28:33 PDT)
Re: [AMBER] Trajectory analysis using pptraj
(Sun May 25 2014 - 03:50:01 PDT)
Re: [AMBER] Trajectory analysis using pptraj
(Thu May 22 2014 - 05:52:19 PDT)
Re: [AMBER] QM/MM tutorial
(Thu May 22 2014 - 05:42:28 PDT)
Re: [AMBER] QM/MM tutorial
(Thu May 22 2014 - 05:10:59 PDT)
Re: [AMBER] QM/MM tutorial
(Thu May 22 2014 - 03:27:02 PDT)
Re: [AMBER] Trajectory analysis using pptraj
(Wed May 21 2014 - 08:19:42 PDT)
[AMBER] Simulation of the protein with internal water
(Wed May 21 2014 - 05:39:02 PDT)
[AMBER] Trajectory analysis using pptraj
(Tue May 20 2014 - 08:05:38 PDT)
[AMBER] Constant protein diffusion across PB boundaties
(Tue May 20 2014 - 01:59:22 PDT)
Re: [AMBER] QM/MM tutorial
(Sun May 18 2014 - 03:49:47 PDT)
Re: [AMBER] QM/MM tutorial
(Fri May 16 2014 - 03:45:20 PDT)
Re: [AMBER] QM/MM tutorial
(Fri May 16 2014 - 03:39:50 PDT)
Re: [AMBER] QM/MM tutorial
(Fri May 16 2014 - 03:05:30 PDT)
Re: [AMBER] QM/MM tutorial
(Fri May 16 2014 - 00:26:15 PDT)
Re: [AMBER] QM/MM tutorial
(Thu May 15 2014 - 04:06:36 PDT)
Re: [AMBER] QM/MM tutorial
(Thu May 15 2014 - 02:33:28 PDT)
Re: [AMBER] QM/MM tutorial
(Wed May 14 2014 - 08:55:33 PDT)
Re: [AMBER] QM/MM tutorial
(Wed May 14 2014 - 08:20:44 PDT)
Re: [AMBER] QM/MM tutorial
(Wed May 14 2014 - 04:00:12 PDT)
Re: [AMBER] QM/MM tutorial
(Wed May 14 2014 - 03:15:10 PDT)
Re: [AMBER] Analysis of the mmpbsa output
(Wed May 14 2014 - 02:42:08 PDT)
Re: [AMBER] QM/MM tutorial
(Wed May 14 2014 - 01:44:08 PDT)
Re: [AMBER] QM/MM tutorial
(Tue May 13 2014 - 06:09:04 PDT)
Re: [AMBER] QM/MM tutorial
(Tue May 13 2014 - 05:02:46 PDT)
Re: [AMBER] Modeling systems with non-standard residues
(Tue May 13 2014 - 04:41:03 PDT)
Re: [AMBER] QM/MM tutorial
(Tue May 13 2014 - 04:34:54 PDT)
[AMBER] QM/MM tutorial
(Mon May 12 2014 - 02:32:14 PDT)
Re: [AMBER] Modeling systems with non-standard residues
(Mon May 12 2014 - 00:05:54 PDT)
Re: [AMBER] Modeling systems with non-standard residues
(Sun May 11 2014 - 03:24:39 PDT)
[AMBER] Analysis of the mmpbsa output
(Sun May 11 2014 - 00:43:44 PDT)
Re: [AMBER] Membrane protein simulation
(Wed May 07 2014 - 23:50:22 PDT)
[AMBER] Modeling systems with non-standard residues
(Wed May 07 2014 - 23:43:15 PDT)
Re: [AMBER] Simulations using pmemd.cuda
(Wed May 07 2014 - 23:36:06 PDT)
Re: [AMBER] Simulations using pmemd.cuda
(Wed May 07 2014 - 03:39:12 PDT)
Re: [AMBER] Simulations using pmemd.cuda
(Wed May 07 2014 - 03:18:00 PDT)
[AMBER] Simulations using pmemd.cuda
(Wed May 07 2014 - 02:31:53 PDT)
Re: [AMBER] Problem with the amber-14 compilation on Debian
(Tue May 06 2014 - 07:04:22 PDT)
[AMBER] Membrane protein simulation
(Tue May 06 2014 - 03:15:29 PDT)
[AMBER] Problem with the amber-14 compilation on Debian
(Tue May 06 2014 - 00:09:37 PDT)
Re: [AMBER] Problems with the Amber-14 compilation with CUDA-5.5
(Sat May 03 2014 - 00:10:44 PDT)
Re: [AMBER] Problems with the Amber-14 compilation with CUDA-5.5
(Thu May 01 2014 - 07:19:30 PDT)
Re: [AMBER] Problems with the Amber-14 compilation with CUDA-5.5
(Thu May 01 2014 - 07:17:15 PDT)
Re: [AMBER] Problems with the Amber-14 compilation with CUDA-5.5
(Thu May 01 2014 - 07:06:05 PDT)
Re: [AMBER] Problems with the Amber-14 compilation with CUDA-5.5
(Thu May 01 2014 - 06:47:32 PDT)
Re: [AMBER] Problems during installation of amber-14 with cuda-5 on GTX 670
(Thu May 01 2014 - 02:05:27 PDT)
[AMBER] Problems with the Amber-14 compilation with CUDA-5.5
(Thu May 01 2014 - 00:03:22 PDT)
Jan-Philip Gehrcke
Re: [AMBER] pbsa: solvation radius from topology file not used when radiopt=0
(Sat May 24 2014 - 10:37:25 PDT)
Jason Swails
Re: [AMBER] ff99SB-ildn-nmr
(Sat May 31 2014 - 11:59:30 PDT)
Re: [AMBER] problem using pmemd.cuda with barostat=2 option
(Sat May 31 2014 - 08:51:25 PDT)
Re: [AMBER] request for help in plotting distance matrix plot
(Sat May 31 2014 - 08:00:17 PDT)
Re: [AMBER] Parametrization of non-standart residues
(Sat May 31 2014 - 07:53:51 PDT)
Re: [AMBER] Parametrization of non-standart residues
(Fri May 30 2014 - 11:25:47 PDT)
Re: [AMBER] amber in namd
(Fri May 30 2014 - 08:58:12 PDT)
Re: [AMBER] Alanine Scanning MMPBSA
(Fri May 30 2014 - 08:16:22 PDT)
Re: [AMBER] Alanine Scanning MMPBSA
(Fri May 30 2014 - 08:11:17 PDT)
Re: [AMBER] protonate question
(Fri May 30 2014 - 06:30:13 PDT)
Re: [AMBER] Problem in restarting simulation from restart file
(Fri May 30 2014 - 05:44:50 PDT)
Re: [AMBER] MMPBSA
(Thu May 29 2014 - 12:40:20 PDT)
Re: [AMBER] MMPBSA
(Thu May 29 2014 - 12:07:09 PDT)
Re: [AMBER] Query regarding Amber Advance Tutorial 17
(Thu May 29 2014 - 05:01:17 PDT)
Re: [AMBER] Contributing new water models
(Wed May 28 2014 - 12:22:15 PDT)
Re: [AMBER] amber in namd
(Wed May 28 2014 - 08:41:54 PDT)
Re: [AMBER] 3NKB5
(Wed May 28 2014 - 08:12:39 PDT)
Re: [AMBER] 3NKB5
(Wed May 28 2014 - 07:29:13 PDT)
Re: [AMBER] Alanine Scanning MMPBSA
(Wed May 28 2014 - 06:52:26 PDT)
Re: [AMBER] command to check non bonded interactions like vander waal's interactions
(Wed May 28 2014 - 06:37:26 PDT)
Re: [AMBER] print residue
(Wed May 28 2014 - 05:03:20 PDT)
Re: [AMBER] OpenMM Performance (was Re: in vacuo dynamics)
(Tue May 27 2014 - 19:14:38 PDT)
Re: [AMBER] in vacuo dynamics
(Tue May 27 2014 - 06:19:37 PDT)
Re: [AMBER] Residue Pairing ih MMPBSA calculation
(Tue May 27 2014 - 03:21:57 PDT)
Re: [AMBER] 3NKB5
(Tue May 27 2014 - 03:20:14 PDT)
[AMBER] OpenMM Performance (was Re: in vacuo dynamics)
(Mon May 26 2014 - 15:35:44 PDT)
Re: [AMBER] How to define the direction of the force in SMD method?
(Mon May 26 2014 - 12:36:08 PDT)
Re: [AMBER] in vacuo dynamics
(Mon May 26 2014 - 12:30:48 PDT)
Re: [AMBER] in vacuo dynamics
(Mon May 26 2014 - 12:21:59 PDT)
Re: [AMBER] MD at constant pH and high temperature
(Mon May 26 2014 - 12:10:07 PDT)
Re: [AMBER] Topology and Corresponding PDB Amber
(Sat May 24 2014 - 13:37:47 PDT)
Re: [AMBER] in vacuo dynamics
(Fri May 23 2014 - 07:41:01 PDT)
Re: [AMBER] Problem in loading leaprc.zinc
(Fri May 23 2014 - 05:23:57 PDT)
Re: [AMBER] SASA calculation
(Fri May 23 2014 - 05:16:42 PDT)
Re: [AMBER] in vacuo dynamics
(Fri May 23 2014 - 05:11:58 PDT)
Re: [AMBER] prmtop error
(Thu May 22 2014 - 19:15:38 PDT)
Re: [AMBER] prmtop error
(Thu May 22 2014 - 14:45:39 PDT)
Re: [AMBER] in vacuo dynamics
(Thu May 22 2014 - 14:42:36 PDT)
Re: [AMBER] mmpbsa
(Thu May 22 2014 - 08:31:53 PDT)
Re: [AMBER] QM/MM tutorial
(Thu May 22 2014 - 06:50:24 PDT)
Re: [AMBER] Trajectory analysis using pptraj
(Thu May 22 2014 - 06:22:44 PDT)
Re: [AMBER] QM/MM tutorial
(Thu May 22 2014 - 05:34:35 PDT)
Re: [AMBER] antechamber error
(Thu May 22 2014 - 04:36:23 PDT)
Re: [AMBER] QM/MM tutorial
(Thu May 22 2014 - 04:29:19 PDT)
Re: [AMBER] Interactions across the periodic box boundaries
(Wed May 21 2014 - 14:45:52 PDT)
Re: [AMBER] Temperature rises to 4000K during NVT equilibration
(Wed May 21 2014 - 08:40:51 PDT)
Re: [AMBER] Trajectory analysis using pptraj
(Wed May 21 2014 - 08:38:27 PDT)
Re: [AMBER] ALA and NALA charges in Amber03 and Amber99
(Wed May 21 2014 - 07:38:34 PDT)
Re: [AMBER] conversion force constant
(Wed May 21 2014 - 05:25:42 PDT)
Re: [AMBER] cant run ntp=3 without csurften
(Tue May 20 2014 - 10:11:40 PDT)
Re: [AMBER] Problem in parallel version of pmemd.cuda
(Tue May 20 2014 - 10:04:39 PDT)
Re: [AMBER] sqm convergence failure
(Tue May 20 2014 - 09:00:02 PDT)
Re: [AMBER] Problem in parallel version of pmemd.cuda
(Tue May 20 2014 - 08:31:41 PDT)
Re: [AMBER] Problem in parallel version of pmemd.cuda
(Tue May 20 2014 - 06:40:37 PDT)
Re: [AMBER] Alanine Scanning MMPBSA
(Tue May 20 2014 - 06:33:04 PDT)
Re: [AMBER] 答复: About the reproducibility of pmemd
(Tue May 20 2014 - 06:30:29 PDT)
Re: [AMBER] Fwd: MMPBSA
(Tue May 20 2014 - 05:45:04 PDT)
Re: [AMBER] Constant protein diffusion across PB boundaties
(Tue May 20 2014 - 04:32:30 PDT)
Re: [AMBER] Constant protein diffusion across PB boundaties
(Tue May 20 2014 - 04:30:41 PDT)
Re: [AMBER] Fwd: MMPBSA
(Tue May 20 2014 - 04:28:21 PDT)
Re: [AMBER] Fwd: MMPBSA
(Mon May 19 2014 - 05:55:18 PDT)
Re: [AMBER] About the reproducibility of pmemd
(Mon May 19 2014 - 05:48:38 PDT)
Re: [AMBER] Unit cell vectors are NOT rotated; imaging will not be possible
(Sat May 17 2014 - 10:49:45 PDT)
Re: [AMBER] Bad prmtop during density run
(Sat May 17 2014 - 10:46:22 PDT)
Re: [AMBER] Problem with Decomposition of Binding Free Energy
(Fri May 16 2014 - 21:06:05 PDT)
Re: [AMBER] Help with ptraj RDF/ion coordination shells/number of ions within regions
(Fri May 16 2014 - 20:56:16 PDT)
Re: [AMBER] Help with ptraj RDF/ion coordination shells/number of ions within regions
(Fri May 16 2014 - 20:50:53 PDT)
Re: [AMBER] acetylated lysine - OXT
(Fri May 16 2014 - 06:46:03 PDT)
Re: [AMBER] Analysis of minimization stage
(Fri May 16 2014 - 06:43:49 PDT)
Re: [AMBER] ALA and NALA charges in Amber03 and Amber99
(Thu May 15 2014 - 09:00:47 PDT)
Re: [AMBER] Analysis of minimization stage
(Thu May 15 2014 - 08:46:54 PDT)
Re: [AMBER] sander and processor
(Thu May 15 2014 - 08:38:05 PDT)
Re: [AMBER] ALA and NALA charges in Amber03 and Amber99
(Thu May 15 2014 - 08:30:10 PDT)
Re: [AMBER] AmberTools 14 compilation on OSX fails
(Thu May 15 2014 - 06:23:35 PDT)
Re: [AMBER] AmberTools 14 compilation on OSX fails
(Thu May 15 2014 - 04:18:20 PDT)
Re: [AMBER] Installation AmberTools13
(Thu May 15 2014 - 04:07:04 PDT)
Re: [AMBER] QM/MM tutorial
(Thu May 15 2014 - 04:00:11 PDT)
Re: [AMBER] Protocol for multiple CPU+ single GPU run on a single node,
(Wed May 14 2014 - 12:33:13 PDT)
Re: [AMBER] Protocol for multiple CPU+ single GPU run on a single node,
(Wed May 14 2014 - 10:34:53 PDT)
Re: [AMBER] Protocol for multiple CPU+ single GPU run on a single node,
(Wed May 14 2014 - 08:17:32 PDT)
Re: [AMBER] get sqm Error when run antechamber
(Wed May 14 2014 - 07:48:34 PDT)
Re: [AMBER] Installation Problem of AmberTools14
(Wed May 14 2014 - 07:42:28 PDT)
Re: [AMBER] AmberTools 14 compilation on OSX fails
(Wed May 14 2014 - 07:34:54 PDT)
Re: [AMBER] Need help as a beginner
(Wed May 14 2014 - 05:52:21 PDT)
Re: [AMBER] Need help as a beginner
(Wed May 14 2014 - 05:25:09 PDT)
Re: [AMBER] QM/MM tutorial
(Wed May 14 2014 - 05:12:17 PDT)
Re: [AMBER] AmberTools 14 compilation on OSX fails
(Wed May 14 2014 - 04:47:24 PDT)
Re: [AMBER] Installation Problem of AmberTools14
(Wed May 14 2014 - 04:45:29 PDT)
Re: [AMBER] Analysis of the mmpbsa output
(Wed May 14 2014 - 04:40:37 PDT)
Re: [AMBER] thermodynamic integration (TI) simulation: pmemd of amber14 vs sander of amber11- vdw transformation
(Wed May 14 2014 - 04:37:01 PDT)
Re: [AMBER] QM/MM tutorial
(Wed May 14 2014 - 04:29:32 PDT)
Re: [AMBER] Need help as a beginner
(Tue May 13 2014 - 15:16:57 PDT)
Re: [AMBER] exctracting indivdual frames into seperate files
(Tue May 13 2014 - 07:00:54 PDT)
Re: [AMBER] REMD velocity information
(Tue May 13 2014 - 06:06:24 PDT)
Re: [AMBER] exctracting indivdual frames into seperate files
(Tue May 13 2014 - 06:01:19 PDT)
Re: [AMBER] Force field of antechamber , parm94 ? parm99?
(Tue May 13 2014 - 04:40:07 PDT)
Re: [AMBER] Urgent: unable to generate files
(Tue May 13 2014 - 04:37:30 PDT)
Re: [AMBER] Alanine Scanning MMPBSA
(Tue May 13 2014 - 04:27:13 PDT)
Re: [AMBER] Recompile amber12 whit cuda 6.0
(Mon May 12 2014 - 12:18:17 PDT)
Re: [AMBER] about GPU memory requirements
(Mon May 12 2014 - 12:14:32 PDT)
Re: [AMBER] Force field of antechamber , parm94 ? parm99?
(Mon May 12 2014 - 07:56:35 PDT)
Re: [AMBER] Analysis of minimization stage
(Mon May 12 2014 - 07:18:47 PDT)
Re: [AMBER] Analysis of minimization stage
(Mon May 12 2014 - 06:22:05 PDT)
Re: [AMBER] Analysis of the mmpbsa output
(Mon May 12 2014 - 04:52:22 PDT)
Re: [AMBER] Modeling systems with non-standard residues
(Mon May 12 2014 - 04:41:33 PDT)
Re: [AMBER] Analysis of minimization stage
(Mon May 12 2014 - 04:39:03 PDT)
Re: [AMBER] Force field of antechamber , parm94 ? parm99?
(Mon May 12 2014 - 04:32:58 PDT)
Re: [AMBER] QM/MM tutorial
(Mon May 12 2014 - 04:13:33 PDT)
Re: [AMBER] sqm convergence failure
(Mon May 12 2014 - 04:10:35 PDT)
Re: [AMBER] multinode NPT runs on GPU
(Fri May 09 2014 - 08:32:56 PDT)
Re: [AMBER] multinode NPT runs on GPU
(Fri May 09 2014 - 07:00:29 PDT)
Re: [AMBER] delta Ggas and Delta Gsolv
(Fri May 09 2014 - 06:40:53 PDT)
Re: [AMBER] Siginificance of delta G
(Fri May 09 2014 - 06:36:52 PDT)
Re: [AMBER] multinode NPT runs on GPU
(Fri May 09 2014 - 06:34:56 PDT)
Re: [AMBER] Alanine Scanning MMPBSA
(Fri May 09 2014 - 04:43:19 PDT)
Re: [AMBER] Regarding Calculation of Hydrogen Bond Energy
(Thu May 08 2014 - 11:42:20 PDT)
Re: [AMBER] Alanine Scanning MMPBSA
(Thu May 08 2014 - 10:19:36 PDT)
Re: [AMBER] syntax error and nab2c failed when using NAB
(Thu May 08 2014 - 06:41:20 PDT)
Re: [AMBER] sqm convergence failure
(Thu May 08 2014 - 06:25:02 PDT)
Re: [AMBER] syntax error and nab2c failed when using NAB
(Thu May 08 2014 - 05:54:43 PDT)
Re: [AMBER] syntax error and nab2c failed when using NAB
(Thu May 08 2014 - 05:23:40 PDT)
Re: [AMBER] sqm convergence failure
(Thu May 08 2014 - 05:22:41 PDT)
Re: [AMBER] syntax error and nab2c failed when using NAB
(Thu May 08 2014 - 04:56:49 PDT)
Re: [AMBER] valve of VDW too high
(Thu May 08 2014 - 04:41:34 PDT)
Re: [AMBER] Defining memory for QM/MM calculations
(Thu May 08 2014 - 04:29:23 PDT)
Re: [AMBER] SolvateBox command
(Thu May 08 2014 - 04:25:42 PDT)
Re: [AMBER] Modeling systems with non-standard residues
(Thu May 08 2014 - 04:17:18 PDT)
Re: [AMBER] please let me unsubscribe of this
(Thu May 08 2014 - 04:12:46 PDT)
Re: [AMBER] error in equilibration
(Wed May 07 2014 - 07:21:29 PDT)
Re: [AMBER] re-imaging bilayer
(Wed May 07 2014 - 05:36:41 PDT)
Re: [AMBER] Amber12 parallel installation error with MPICH2 UBUNTU 14.04
(Wed May 07 2014 - 05:04:37 PDT)
Re: [AMBER] PDB for 1-octanol molecules
(Wed May 07 2014 - 04:55:04 PDT)
Re: [AMBER] "cudaDeviceEnablePeerAccess all CUDA-capable devices are busy or unavailable"
(Wed May 07 2014 - 04:37:55 PDT)
Re: [AMBER] Simulations using pmemd.cuda
(Wed May 07 2014 - 04:34:15 PDT)
Re: [AMBER] MMPBSA & mmpbsa_py_nabnmode frequent crashes
(Tue May 06 2014 - 18:53:01 PDT)
Re: [AMBER] dihedrals in CYT residue
(Tue May 06 2014 - 10:33:28 PDT)
Re: [AMBER] Problem with the amber-14 compilation on Debian
(Tue May 06 2014 - 07:55:47 PDT)
Re: [AMBER] Pairwise interaction energy between each residue
(Tue May 06 2014 - 07:26:24 PDT)
Re: [AMBER] Problem with the amber-14 compilation on Debian
(Tue May 06 2014 - 05:05:15 PDT)
Re: [AMBER] Membrane protein simulation
(Tue May 06 2014 - 04:57:52 PDT)
Re: [AMBER] Extract MD co-ordinates
(Mon May 05 2014 - 10:56:45 PDT)
Re: [AMBER] Percent Occupancy with PCA
(Mon May 05 2014 - 08:50:50 PDT)
Re: [AMBER] Installation of AmberTools13
(Mon May 05 2014 - 08:47:58 PDT)
Re: [AMBER] Extract velocity from the restart file
(Mon May 05 2014 - 07:13:10 PDT)
Re: [AMBER] acpype on ambertools13
(Mon May 05 2014 - 04:18:57 PDT)
Re: [AMBER] acpype on ambertools13
(Mon May 05 2014 - 03:08:31 PDT)
Re: [AMBER] psf generation
(Mon May 05 2014 - 03:06:13 PDT)
Re: [AMBER] Intermittent error during T-REMD on 8 GPU computer
(Fri May 02 2014 - 08:16:20 PDT)
Re: [AMBER] Parameters for FAD
(Fri May 02 2014 - 04:40:01 PDT)
Re: [AMBER] Parameters for FAD
(Thu May 01 2014 - 12:20:38 PDT)
Re: [AMBER] Problems with the Amber-14 compilation with CUDA-5.5
(Thu May 01 2014 - 07:25:57 PDT)
Re: [AMBER] Problems during installation of amber-14 with cuda-5 on GTX 670
(Thu May 01 2014 - 06:15:49 PDT)
Jinfeng Huang
Re: [AMBER] Force field of antechamber , parm94 ? parm99?
(Tue May 13 2014 - 03:14:48 PDT)
Re: [AMBER] Force field of antechamber , parm94 ? parm99?
(Mon May 12 2014 - 07:24:58 PDT)
[AMBER] Force field of antechamber , parm94 ? parm99?
(Mon May 12 2014 - 02:22:57 PDT)
Josh Berryman
Re: [AMBER] Problems during installation of amber-14 with cuda-5 on GTX 670
(Thu May 01 2014 - 23:45:19 PDT)
Re: [AMBER] Problems during installation of amber-14 with cuda-5 on GTX 670
(Thu May 01 2014 - 23:43:39 PDT)
Keiran Rowell
Re: [AMBER] GTX780Ti consistent error "cudaMemcpy GpuBuffer::Download failed unspecified launch failure."
(Thu May 29 2014 - 22:43:53 PDT)
Kim TaeHwan
[AMBER] I want to know about formula of RESP Charge in the Amber
(Sat May 24 2014 - 08:43:39 PDT)
kirtana S
[AMBER] solvating molecule
(Thu May 01 2014 - 18:26:36 PDT)
Kshatresh Dutta Dubey
[AMBER] Problem in restarting simulation from restart file
(Fri May 30 2014 - 05:04:59 PDT)
Re: [AMBER] Query regarding Amber Advance Tutorial 17
(Thu May 29 2014 - 06:54:23 PDT)
[AMBER] Query regarding Amber Advance Tutorial 17
(Thu May 29 2014 - 01:54:51 PDT)
[AMBER] Bad prmtop during density run
(Sat May 17 2014 - 09:17:03 PDT)
Re: [AMBER] Defining memory for QM/MM calculations
(Thu May 08 2014 - 05:02:30 PDT)
[AMBER] Defining memory for QM/MM calculations
(Thu May 08 2014 - 02:40:48 PDT)
kurisaki
Re: [AMBER] Prepareing branched residue
(Tue May 06 2014 - 19:19:04 PDT)
[AMBER] Prepareing branched residue
(Thu May 01 2014 - 22:57:23 PDT)
Lachele Foley
[AMBER] Announcement: New GLYCAM-Web
(Mon May 19 2014 - 14:40:55 PDT)
Lara rajam
[AMBER] amber in namd
(Fri May 30 2014 - 08:46:40 PDT)
[AMBER] amber in namd
(Wed May 28 2014 - 08:21:53 PDT)
[AMBER] prmtop error
(Thu May 22 2014 - 12:08:41 PDT)
[AMBER] mmpbsa
(Thu May 22 2014 - 11:41:16 PDT)
[AMBER] error in equilibration
(Wed May 07 2014 - 07:03:23 PDT)
Lee-Ping Wang
Re: [AMBER] Contributing new water models
(Wed May 28 2014 - 12:26:43 PDT)
[AMBER] Contributing new water models
(Wed May 28 2014 - 11:35:30 PDT)
liu junjun
Re: [AMBER] Urgent: unable to generate files
(Tue May 13 2014 - 03:49:36 PDT)
Re: [AMBER] get sqm Error when run antechamber
(Tue May 13 2014 - 03:32:46 PDT)
loue chen
[AMBER] Problem with Decomposition of Binding Free Energy
(Fri May 16 2014 - 12:08:46 PDT)
M. Reza Ganjalikhany
Re: [AMBER] Amber12 parallel installation error with MPICH2 UBUNTU 14.04
(Sat May 10 2014 - 12:09:08 PDT)
Re: [AMBER] Amber12 parallel installation error with MPICH2 UBUNTU 14.04
(Fri May 09 2014 - 23:09:08 PDT)
[AMBER] Amber12 parallel installation error with MPICH2 UBUNTU 14.04
(Wed May 07 2014 - 01:32:52 PDT)
mahnam karim
[AMBER] MMPBSA_complex.mdcrd.0 error
(Thu May 29 2014 - 07:03:58 PDT)
Manikanthan Bhavaraju
Re: [AMBER] Scaling of atomic mass of water molecules
(Tue May 13 2014 - 10:45:47 PDT)
Re: [AMBER] Scaling of atomic mass of water molecules
(Tue May 13 2014 - 10:05:22 PDT)
Re: [AMBER] Scaling of atomic mass of water molecules
(Tue May 13 2014 - 08:37:55 PDT)
Re: [AMBER] Scaling of atomic mass of water molecules
(Tue May 13 2014 - 08:26:26 PDT)
Re: [AMBER] Scaling of atomic mass of water molecules
(Tue May 13 2014 - 08:16:41 PDT)
[AMBER] Scaling of atomic mass of water molecules
(Tue May 13 2014 - 07:51:44 PDT)
Marc van der Kamp
Re: [AMBER] SQM: How to extract the charge density of sqm runs?
(Tue May 20 2014 - 02:35:26 PDT)
Re: [AMBER] QM/MM tutorial
(Mon May 19 2014 - 05:06:56 PDT)
Re: [AMBER] QM/MM tutorial
(Fri May 16 2014 - 04:18:03 PDT)
Re: [AMBER] QM/MM tutorial
(Fri May 16 2014 - 03:33:28 PDT)
Re: [AMBER] QM/MM tutorial
(Wed May 14 2014 - 05:00:00 PDT)
Re: [AMBER] QM/MM tutorial
(Tue May 13 2014 - 07:06:03 PDT)
Re: [AMBER] QM/MM tutorial
(Tue May 13 2014 - 05:42:52 PDT)
Re: [AMBER] QM/MM tutorial
(Tue May 13 2014 - 04:39:28 PDT)
Re: [AMBER] Simulations using pmemd.cuda
(Wed May 07 2014 - 03:10:34 PDT)
Marek Maly
Re: [AMBER] Empirical force fields: release new version of RED Server Dev/PyRED
(Wed May 07 2014 - 12:13:45 PDT)
Re: [AMBER] Empirical force fields: release new version of RED Server Dev/PyRED
(Wed May 07 2014 - 09:22:40 PDT)
Re: [AMBER] Empirical force fields: release new version of RED Server Dev/PyRED
(Tue May 06 2014 - 15:06:49 PDT)
Re: [AMBER] Empirical force fields: release new version of RED Server Dev/PyRED
(Mon May 05 2014 - 06:22:56 PDT)
Mari Mak
[AMBER] PDB for 1-octanol molecules
(Tue May 06 2014 - 23:13:18 PDT)
Mark Williamson
Re: [AMBER] QM/MM tutorial
(Wed May 14 2014 - 02:12:43 PDT)
Marlet Martinez
Re: [AMBER] secondary structure calculation using Cpptraj
(Wed May 21 2014 - 00:30:54 PDT)
[AMBER] secondary structure calculation using Cpptraj
(Tue May 20 2014 - 13:00:20 PDT)
Massimiliano Porrini
Re: [AMBER] in vacuo dynamics
(Tue May 27 2014 - 06:40:46 PDT)
Re: [AMBER] in vacuo dynamics
(Tue May 27 2014 - 06:04:49 PDT)
Re: [AMBER] in vacuo dynamics
(Mon May 26 2014 - 03:34:20 PDT)
Re: [AMBER] in vacuo dynamics
(Sun May 25 2014 - 06:42:50 PDT)
Re: [AMBER] in vacuo dynamics
(Fri May 23 2014 - 07:06:00 PDT)
Re: [AMBER] in vacuo dynamics
(Fri May 23 2014 - 03:30:37 PDT)
Re: [AMBER] in vacuo dynamics
(Fri May 23 2014 - 03:18:44 PDT)
[AMBER] in vacuo dynamics
(Thu May 22 2014 - 12:52:26 PDT)
Milo Westler
Re: [AMBER] Intermittent error during T-REMD on 8 GPU computer
(Fri May 02 2014 - 08:33:05 PDT)
[AMBER] Intermittent error during T-REMD on 8 GPU computer
(Fri May 02 2014 - 07:33:48 PDT)
MOHD HOMAIDUR RAHMAN
[AMBER] Regarding Calculation of Hydrogen Bond Energy
(Thu May 08 2014 - 11:00:50 PDT)
[AMBER] Pairwise interaction energy between each residue
(Tue May 06 2014 - 00:28:04 PDT)
[AMBER] Regarding Calculation of Hydrogen Bond Energy
(Mon May 05 2014 - 23:30:05 PDT)
MURAT OZTURK
Re: [AMBER] Protocol for multiple CPU+ single GPU run on a single node,
(Wed May 14 2014 - 12:41:37 PDT)
Re: [AMBER] Protocol for multiple CPU+ single GPU run on a single node,
(Wed May 14 2014 - 12:22:24 PDT)
Re: [AMBER] Protocol for multiple CPU+ single GPU run on a single node,
(Wed May 14 2014 - 11:35:26 PDT)
Re: [AMBER] Protocol for multiple CPU+ single GPU run on a single node,
(Wed May 14 2014 - 10:13:25 PDT)
[AMBER] Protocol for multiple CPU+ single GPU run on a single node,
(Wed May 14 2014 - 07:49:16 PDT)
Re: [AMBER] Need help as a beginner
(Wed May 14 2014 - 05:44:08 PDT)
Re: [AMBER] Need help as a beginner
(Wed May 14 2014 - 05:42:54 PDT)
Re: [AMBER] Need help as a beginner
(Tue May 13 2014 - 16:02:53 PDT)
Re: [AMBER] Need help as a beginner
(Tue May 13 2014 - 13:47:35 PDT)
Re: [AMBER] Need help as a beginner
(Tue May 13 2014 - 13:17:49 PDT)
[AMBER] Need help as a beginner
(Tue May 13 2014 - 12:31:59 PDT)
Nash, Anthony
[AMBER] zinc partial charges
(Tue May 27 2014 - 23:30:38 PDT)
Nelson Max
[AMBER] Attempting to modify Amber
(Tue May 20 2014 - 17:47:39 PDT)
newamber list
Re: [AMBER] handling long trajs for PCA and components plot
(Wed May 21 2014 - 14:07:02 PDT)
Re: [AMBER] Unit cell vectors are NOT rotated; imaging will not be possible
(Sat May 17 2014 - 11:09:56 PDT)
[AMBER] Unit cell vectors are NOT rotated; imaging will not be possible
(Sat May 17 2014 - 09:41:38 PDT)
Re: [AMBER] pairwise option in cpptraj
(Thu May 15 2014 - 12:14:40 PDT)
[AMBER] pairwise option in cpptraj
(Thu May 15 2014 - 10:25:28 PDT)
[AMBER] when nastruct does NOT print the basepair information
(Thu May 15 2014 - 07:52:04 PDT)
Re: [AMBER] handling long trajs for PCA and components plot
(Sun May 11 2014 - 12:10:13 PDT)
Re: [AMBER] Analysis of evecs.dat file
(Fri May 09 2014 - 10:52:11 PDT)
Re: [AMBER] handling long trajs for PCA and components plot
(Wed May 07 2014 - 15:27:25 PDT)
Re: [AMBER] handling long trajs for PCA and components plot
(Tue May 06 2014 - 21:21:41 PDT)
Re: [AMBER] handling long trajs for PCA and components plot
(Tue May 06 2014 - 19:13:37 PDT)
[AMBER] handling long trajs for PCA and components plot
(Mon May 05 2014 - 16:23:26 PDT)
Nicole Ippolito
Re: [AMBER] Percent Occupancey with PCA
(Mon May 05 2014 - 08:28:27 PDT)
[AMBER] Percent Occupancy with PCA
(Mon May 05 2014 - 08:25:26 PDT)
[AMBER] Percent Occupancey with PCA
(Fri May 02 2014 - 08:17:34 PDT)
Nihal Korkmaz
[AMBER] ff99SB-ildn-nmr
(Sat May 31 2014 - 11:44:23 PDT)
[AMBER] PMF as a function of Q, fraction of native contacts
(Mon May 05 2014 - 15:47:13 PDT)
Nitin Sharma
[AMBER] command to check non bonded interactions like vander waal's interactions
(Wed May 28 2014 - 06:27:12 PDT)
Re: [AMBER] QM/MM based binding free energy analysis AMBER
(Mon May 19 2014 - 02:53:24 PDT)
Re: [AMBER] QM/MM based binding free energy analysis AMBER
(Sun May 18 2014 - 13:00:26 PDT)
Re: [AMBER] QM/MM based binding free energy analysis AMBER
(Sun May 18 2014 - 12:38:26 PDT)
Re: [AMBER] exctracting indivdual frames into seperate files
(Tue May 13 2014 - 07:01:39 PDT)
Re: [AMBER] exctracting indivdual frames into seperate files
(Tue May 13 2014 - 06:40:56 PDT)
[AMBER] exctracting indivdual frames into seperate files
(Tue May 13 2014 - 05:54:09 PDT)
Re: [AMBER] number of frames in MMPBGBSA
(Tue May 06 2014 - 08:38:06 PDT)
[AMBER] number of frames in MMPBGBSA
(Tue May 06 2014 - 05:15:24 PDT)
Re: [AMBER] alanine scanning
(Sun May 04 2014 - 08:29:30 PDT)
[AMBER] alanine scanning
(Sat May 03 2014 - 06:47:35 PDT)
Norbert GARNIER
Re: [AMBER] FapydG parameters
(Wed May 07 2014 - 07:02:58 PDT)
[AMBER] FapydG parameters
(Wed May 07 2014 - 05:30:27 PDT)
Parker de Waal
Re: [AMBER] Parametrization of non-standart residues
(Sat May 31 2014 - 05:50:12 PDT)
Re: [AMBER] Parametrization of non-standart residues
(Fri May 30 2014 - 12:43:16 PDT)
Re: [AMBER] Modeling systems with non-standard residues
(Mon May 12 2014 - 04:31:30 PDT)
Paulsen, Janet
[AMBER] periodic box buffer zone
(Fri May 30 2014 - 08:35:34 PDT)
Pierpaolo Cacciotto
[AMBER] z-axis restraints
(Thu May 22 2014 - 06:49:37 PDT)
Quynh Vo
Re: [AMBER] vlimit exceeded error when switch from NPT to NVE
(Sun May 04 2014 - 11:06:42 PDT)
[AMBER] vlimit exceeded error when switch from NPT to NVE
(Sat May 03 2014 - 22:39:22 PDT)
Ray Luo, Ph.D.
Re: [AMBER] MMPBSA
(Thu May 29 2014 - 15:53:02 PDT)
Re: [AMBER] MMPBSA_complex.mdcrd.0 error
(Thu May 29 2014 - 10:01:30 PDT)
Re: [AMBER] MMPBSA
(Thu May 29 2014 - 09:44:56 PDT)
Re: [AMBER] MMPBSA
(Wed May 28 2014 - 16:22:04 PDT)
Re: [AMBER] MMPBSA
(Tue May 27 2014 - 12:41:24 PDT)
Re: [AMBER] pbsa: solvation radius from topology file not used when radiopt=0
(Sat May 24 2014 - 11:52:15 PDT)
Re: [AMBER] Error when using PB implicit solvent in XMIN in NAB(PB Bomb in pb_init(): Allocation aborted)
(Fri May 09 2014 - 12:19:28 PDT)
Robert Konecny
Re: [AMBER] compiling iAPBS and sander.APBS?
(Sun May 25 2014 - 19:44:05 PDT)
Re: [AMBER] compiling iAPBS and sander.APBS?
(Sat May 24 2014 - 19:54:28 PDT)
Robert McGibbon
Re: [AMBER] OpenMM Performance (was Re: in vacuo dynamics)
(Tue May 27 2014 - 14:11:41 PDT)
Re: [AMBER] in vacuo dynamics
(Mon May 26 2014 - 14:09:13 PDT)
Re: [AMBER] in vacuo dynamics
(Sun May 25 2014 - 12:30:49 PDT)
Robin Jain
[AMBER] request for help in plotting distance matrix plot
(Fri May 30 2014 - 23:10:22 PDT)
Rodriguez, Yoel
[AMBER] MMPBSA: Per Residue vs Pairwise decomposition Calculation(idecomp= 2 o idecomp=4)
(Tue May 27 2014 - 10:22:06 PDT)
[AMBER] MMPBSA: Per Residue vs Pairwise decomposition Calculation
(Mon May 26 2014 - 18:01:44 PDT)
Ross Walker
Re: [AMBER] GTX780Ti consistent error "cudaMemcpy GpuBuffer::Download failed unspecified launch failure."
(Fri May 30 2014 - 08:42:42 PDT)
Re: [AMBER] QM/MM tutorial
(Thu May 22 2014 - 06:49:52 PDT)
Re: [AMBER] About the chamber in Ambertools 14
(Wed May 21 2014 - 20:31:09 PDT)
Re: [AMBER] cant run ntp=3 without csurften
(Tue May 20 2014 - 13:27:33 PDT)
Re: [AMBER] cant run ntp=3 without csurften
(Tue May 20 2014 - 12:24:49 PDT)
Re: [AMBER] About the reproducibility of pmemd
(Mon May 19 2014 - 11:23:46 PDT)
Re: [AMBER] Problem in parallel version of pmemd.cuda
(Mon May 19 2014 - 11:25:59 PDT)
[AMBER] AMBER Workshop Jun 2nd to 6th - Barcelona - Small number of additional places available.
(Thu May 15 2014 - 12:03:04 PDT)
Re: [AMBER] TI(amber14's pmemd.cuda) on GPUs RE: thermodynamic integration (TI) simulation: pmemd of amber14 vs sander of amber11- vdw transformation
(Wed May 14 2014 - 21:16:29 PDT)
Re: [AMBER] Protocol for multiple CPU+ single GPU run on a single node,
(Wed May 14 2014 - 12:49:10 PDT)
Re: [AMBER] Protocol for multiple CPU+ single GPU run on a single node,
(Wed May 14 2014 - 12:36:11 PDT)
Re: [AMBER] Protocol for multiple CPU+ single GPU run on a single node,
(Wed May 14 2014 - 11:49:41 PDT)
Re: [AMBER] about GPU memory requirements
(Wed May 14 2014 - 10:46:18 PDT)
Re: [AMBER] Protocol for multiple CPU+ single GPU run on a single node,
(Wed May 14 2014 - 10:39:22 PDT)
Re: [AMBER] Protocol for multiple CPU+ single GPU run on a single node,
(Wed May 14 2014 - 08:57:33 PDT)
Re: [AMBER] thermodynamic integration (TI) simulation: pmemd of amber14 vs sander of amber11- vdw transformation
(Wed May 14 2014 - 08:05:39 PDT)
Re: [AMBER] about GPU memory requirements
(Tue May 13 2014 - 14:21:37 PDT)
Re: [AMBER] about GPU memory requirements
(Mon May 12 2014 - 12:20:59 PDT)
Re: [AMBER] Recompile amber12 whit cuda 6.0
(Mon May 12 2014 - 12:17:24 PDT)
Re: [AMBER] Error: invalid argument launching kernel kNLGenerateSpatialHash
(Thu May 08 2014 - 02:00:50 PDT)
Re: [AMBER] "cudaDeviceEnablePeerAccess all CUDA-capable devices are busy or unavailable"
(Thu May 08 2014 - 01:59:05 PDT)
Re: [AMBER] Membrane protein simulation
(Thu May 08 2014 - 00:04:46 PDT)
Re: [AMBER] "cudaDeviceEnablePeerAccess all CUDA-capable devices are busy or unavailable"
(Thu May 08 2014 - 00:00:46 PDT)
Re: [AMBER] Simulations using pmemd.cuda
(Wed May 07 2014 - 08:44:36 PDT)
Re: [AMBER] "cudaDeviceEnablePeerAccess all CUDA-capable devices are busy or unavailable"
(Wed May 07 2014 - 08:41:02 PDT)
Rossen Apostolov
Re: [AMBER] ALA and NALA charges in Amber03 and Amber99
(Wed May 21 2014 - 07:14:26 PDT)
Re: [AMBER] ALA and NALA charges in Amber03 and Amber99
(Thu May 15 2014 - 08:44:19 PDT)
[AMBER] ALA and NALA charges in Amber03 and Amber99
(Thu May 15 2014 - 07:05:22 PDT)
Saba Sulaiman
[AMBER] Amber workshops coming soon ?
(Sun May 11 2014 - 22:51:22 PDT)
Saikat Dutta Chowdhury
[AMBER] REMD velocity information
(Tue May 13 2014 - 05:05:08 PDT)
Sajda Ashraf
[AMBER] antechamber error
(Thu May 22 2014 - 03:53:39 PDT)
[AMBER] error in mdcrd file
(Tue May 20 2014 - 22:48:42 PDT)
Re: [AMBER] error in minimization
(Sun May 18 2014 - 22:21:02 PDT)
[AMBER] error in minimization
(Fri May 16 2014 - 23:48:21 PDT)
sammia khatak
Re: [AMBER] sander restart
(Mon May 19 2014 - 02:55:22 PDT)
Re: [AMBER] sander restart
(Mon May 19 2014 - 02:25:09 PDT)
[AMBER] sander restart
(Sun May 18 2014 - 23:57:15 PDT)
[AMBER] sander and processor
(Thu May 15 2014 - 07:09:14 PDT)
[AMBER] psf generation
(Mon May 05 2014 - 01:44:42 PDT)
[AMBER] sander?
(Sat May 03 2014 - 23:37:16 PDT)
Sangita Kachhap
Re: [AMBER] MD at constant pH and high temperature
(Tue May 27 2014 - 09:13:12 PDT)
Re: [AMBER] MD at pH5 and 50-55 degree celcius
(Tue May 27 2014 - 09:12:11 PDT)
Re: [AMBER] MD at constant pH and high temperature
(Mon May 26 2014 - 10:42:49 PDT)
Re: [AMBER] MD at constant pH and high temperature. .
(Mon May 26 2014 - 09:09:05 PDT)
Re: [AMBER] MD at constant pH and high temperature
(Mon May 26 2014 - 07:47:52 PDT)
[AMBER] MD at pH5 and 50-55 degree celcius
(Sun May 25 2014 - 23:47:28 PDT)
[AMBER] MD at constant pH and high temperature
(Sun May 25 2014 - 06:48:41 PDT)
Sanjib Paul
Re: [AMBER] Problem in parallel version of pmemd.cuda
(Tue May 20 2014 - 09:32:09 PDT)
Re: [AMBER] Problem in parallel version of pmemd.cuda
(Tue May 20 2014 - 08:23:29 PDT)
Re: [AMBER] Problem in parallel version of pmemd.cuda
(Tue May 20 2014 - 06:26:59 PDT)
[AMBER] Problem in parallel version of pmemd.cuda
(Mon May 19 2014 - 11:16:41 PDT)
Scott Le Grand
Re: [AMBER] OpenMM Performance (was Re: in vacuo dynamics)
(Tue May 27 2014 - 20:57:03 PDT)
Re: [AMBER] OpenMM Performance (was Re: in vacuo dynamics)
(Tue May 27 2014 - 12:21:18 PDT)
Re: [AMBER] Protocol for multiple CPU+ single GPU run on a single node,
(Wed May 14 2014 - 11:10:13 PDT)
Re: [AMBER] "cudaDeviceEnablePeerAccess all CUDA-capable devices are busy or unavailable"
(Wed May 07 2014 - 10:31:16 PDT)
Sergio R Aragon
Re: [AMBER] Scaling of atomic mass of water molecules
(Tue May 13 2014 - 10:35:18 PDT)
Sidney Elmer
Re: [AMBER] dihedrals in CYT residue
(Tue May 06 2014 - 11:04:48 PDT)
Re: [AMBER] dihedrals in CYT residue
(Tue May 06 2014 - 10:30:14 PDT)
[AMBER] dihedrals in CYT residue
(Tue May 06 2014 - 10:04:16 PDT)
Soumendranath Bhakat
Re: [AMBER] error in plot of interaction energy in xmgrace
(Sat May 31 2014 - 06:54:53 PDT)
Re: [AMBER] request for help in plotting distance matrix plot
(Fri May 30 2014 - 23:29:24 PDT)
Re: [AMBER] sudden and rapid configuration change in NVT simulation
(Fri May 30 2014 - 02:17:51 PDT)
Re: [AMBER] print residue
(Wed May 28 2014 - 23:40:33 PDT)
Re: [AMBER] command to check non bonded interactions like vander waal's interactions
(Wed May 28 2014 - 06:40:18 PDT)
Re: [AMBER] print residue
(Wed May 28 2014 - 05:15:18 PDT)
Re: [AMBER] PCA and the corresponding pdb
(Wed May 28 2014 - 01:08:31 PDT)
Re: [AMBER] Residue Pairing ih MMPBSA calculation
(Tue May 27 2014 - 04:15:53 PDT)
Re: [AMBER] Residue Pairing ih MMPBSA calculation
(Tue May 27 2014 - 04:13:43 PDT)
[AMBER] Topology and Corresponding PDB Amber
(Sat May 24 2014 - 12:39:49 PDT)
Re: [AMBER] SASA error
(Fri May 23 2014 - 08:29:07 PDT)
[AMBER] SASA error
(Fri May 23 2014 - 06:31:13 PDT)
Re: [AMBER] SASA calculation
(Fri May 23 2014 - 06:14:07 PDT)
Re: [AMBER] SASA calculation
(Fri May 23 2014 - 05:29:38 PDT)
[AMBER] SASA calculation
(Fri May 23 2014 - 05:07:53 PDT)
[AMBER] Secondary Structure Script
(Fri May 23 2014 - 03:45:42 PDT)
Re: [AMBER] prmtop error
(Thu May 22 2014 - 12:42:25 PDT)
Re: [AMBER] QM/MM tutorial
(Thu May 22 2014 - 07:09:32 PDT)
Re: [AMBER] QM/MM tutorial
(Thu May 22 2014 - 05:49:38 PDT)
Re: [AMBER] Error in setting irest=1
(Wed May 21 2014 - 00:19:58 PDT)
Re: [AMBER] QM/MM based binding free energy analysis AMBER
(Mon May 19 2014 - 03:23:09 PDT)
Re: [AMBER] sander restart
(Mon May 19 2014 - 03:18:41 PDT)
Re: [AMBER] sander restart
(Mon May 19 2014 - 02:35:10 PDT)
Re: [AMBER] sander restart
(Mon May 19 2014 - 00:28:58 PDT)
Re: [AMBER] QM/MM based binding free energy analysis AMBER
(Sun May 18 2014 - 13:28:46 PDT)
Re: [AMBER] QM/MM based binding free energy analysis AMBER
(Sun May 18 2014 - 12:48:28 PDT)
[AMBER] QM/MM based binding free energy analysis AMBER
(Sun May 18 2014 - 12:29:58 PDT)
Re: [AMBER] MMPBSA
(Sat May 17 2014 - 05:48:50 PDT)
[AMBER] Inputs QM/MM MD and MMGBSA
(Sun May 11 2014 - 12:57:16 PDT)
Re: [AMBER] number of frames in MMPBGBSA
(Tue May 06 2014 - 11:17:02 PDT)
Re: [AMBER] number of frames in MMPBGBSA
(Tue May 06 2014 - 08:22:44 PDT)
Re: [AMBER] Extract MD co-ordinates
(Mon May 05 2014 - 10:28:42 PDT)
[AMBER] Extract MD co-ordinates
(Mon May 05 2014 - 07:19:14 PDT)
Re: [AMBER] psf generation
(Mon May 05 2014 - 01:58:27 PDT)
Soumya Lipsa Rath
Re: [AMBER] Fwd: MMPBSA
(Tue May 20 2014 - 06:36:39 PDT)
Re: [AMBER] Fwd: MMPBSA
(Tue May 20 2014 - 04:49:27 PDT)
Re: [AMBER] Fwd: MMPBSA
(Mon May 19 2014 - 21:31:29 PDT)
[AMBER] Fwd: MMPBSA
(Sun May 18 2014 - 22:19:18 PDT)
[AMBER] MMPBSA
(Sat May 17 2014 - 03:04:38 PDT)
Sourav Purohit
Re: [AMBER] Additional random motion of com for unwrapped trajectory
(Tue May 20 2014 - 04:29:58 PDT)
[AMBER] Additional random motion of com for unwrapped trajectory
(Sat May 10 2014 - 16:23:18 PDT)
Re: [AMBER] multinode NPT runs on GPU
(Fri May 09 2014 - 07:19:06 PDT)
Re: [AMBER] multinode NPT runs on GPU
(Fri May 09 2014 - 06:43:59 PDT)
[AMBER] multinode NPT runs on GPU
(Fri May 09 2014 - 05:50:19 PDT)
Sushi Shilpa
[AMBER] Problem in generating xml param files
(Fri May 16 2014 - 23:06:18 PDT)
Thomas Cheatham
Re: [AMBER] prmtop error
(Thu May 22 2014 - 15:07:07 PDT)
Thomas Evangelidis
Re: [AMBER] about GPU memory requirements
(Wed May 14 2014 - 02:41:15 PDT)
Re: [AMBER] about GPU memory requirements
(Tue May 13 2014 - 14:12:13 PDT)
[AMBER] about GPU memory requirements
(Mon May 12 2014 - 11:58:29 PDT)
Thomas Exner
Re: [AMBER] NH4+
(Wed May 21 2014 - 01:15:26 PDT)
Re: [AMBER] NH4+
(Mon May 19 2014 - 06:00:21 PDT)
[AMBER] NH4+
(Mon May 19 2014 - 05:31:56 PDT)
ujihara.ryuuta.47u.st.kyoto-u.ac.jp
Re: [AMBER] Installation Problem of AmberTools14
(Wed May 14 2014 - 06:09:41 PDT)
[AMBER] Installation Problem of AmberTools14
(Tue May 13 2014 - 21:54:10 PDT)
Val Yu
[AMBER] 答复: About the reproducibility of pmemd
(Tue May 20 2014 - 05:56:53 PDT)
[AMBER] About the reproducibility of pmemd
(Mon May 19 2014 - 05:01:48 PDT)
Valentina D'Atri
Re: [AMBER] how to protonate phosphate groups of nucleotides
(Wed May 28 2014 - 08:59:37 PDT)
Valentina Romano
[AMBER] Error in setting irest=1
(Tue May 20 2014 - 09:14:07 PDT)
Re: [AMBER] Analysis of minimization stage
(Tue May 20 2014 - 06:46:03 PDT)
Re: [AMBER] Analysis of minimization stage
(Fri May 16 2014 - 06:50:49 PDT)
Re: [AMBER] Analysis of minimization stage
(Fri May 16 2014 - 05:58:33 PDT)
Re: [AMBER] Analysis of minimization stage
(Fri May 16 2014 - 04:39:19 PDT)
Re: [AMBER] Analysis of minimization stage
(Thu May 15 2014 - 06:07:43 PDT)
Re: [AMBER] Analysis of minimization stage
(Wed May 14 2014 - 06:58:08 PDT)
Re: [AMBER] Analysis of minimization stage
(Tue May 13 2014 - 07:30:41 PDT)
Re: [AMBER] Analysis of minimization stage
(Tue May 13 2014 - 07:02:11 PDT)
Re: [AMBER] Analysis of minimization stage
(Mon May 12 2014 - 09:26:44 PDT)
Re: [AMBER] Analysis of minimization stage
(Mon May 12 2014 - 07:15:13 PDT)
Re: [AMBER] Analysis of minimization stage
(Mon May 12 2014 - 04:53:26 PDT)
Re: [AMBER] Analysis of minimization stage
(Mon May 12 2014 - 01:47:42 PDT)
Re: [AMBER] Analysis of minimization stage
(Fri May 09 2014 - 09:39:04 PDT)
Re: [AMBER] Analysis of minimization stage
(Fri May 09 2014 - 01:52:04 PDT)
Re: [AMBER] Analysis of minimization stage
(Thu May 08 2014 - 09:32:02 PDT)
[AMBER] Analysis of minimization stage
(Thu May 08 2014 - 09:04:41 PDT)
Vijay Manickam Achari
[AMBER] re-imaging bilayer
(Wed May 07 2014 - 05:00:14 PDT)
Vlad Cojocaru
Re: [AMBER] Loop refirement
(Wed May 28 2014 - 00:53:40 PDT)
Re: [AMBER] Trajectory analysis using pptraj
(Wed May 21 2014 - 08:24:17 PDT)
Xiaoquan Sun
[AMBER] Question about structure factor?
(Wed May 07 2014 - 13:33:53 PDT)
Yeng-Tseng Wang
Re: [AMBER] About the chamber in Ambertools 14
(Thu May 22 2014 - 21:34:04 PDT)
Re: [AMBER] About the chamber in Ambertools 14
(Thu May 22 2014 - 02:19:33 PDT)
[AMBER] About the chamber in Ambertools 14
(Wed May 21 2014 - 18:23:14 PDT)
Yew Mun Yip
Re: [AMBER] How to extract each frame of a trajectory as individual .mdcrd files?
(Wed Apr 30 2014 - 09:05:39 PDT)
Yin, Guowei
Re: [AMBER] Extract velocity from the restart file
(Mon May 05 2014 - 07:16:27 PDT)
Re: [AMBER] Extract velocity from the restart file
(Mon May 05 2014 - 06:39:17 PDT)
Ying-Chieh Sun
[AMBER] TI(amber14's pmemd.cuda) on GPUs RE: thermodynamic integration (TI) simulation: pmemd of amber14 vs sander of amber11- vdw transformation
(Wed May 14 2014 - 20:42:24 PDT)
[AMBER] thermodynamic integration (TI) simulation: pmemd of amber14 vs sander of amber11- vdw transformation
(Wed May 14 2014 - 03:21:17 PDT)
Yip Yew Mun
Re: [AMBER] Script for Calculating RMSIP
(Tue May 20 2014 - 19:33:20 PDT)
[AMBER] Script for Calculating RMSIP
(Sat May 17 2014 - 08:54:30 PDT)
[AMBER] How to plot Eigenvectors against % Positional Fluctuations
(Fri May 16 2014 - 21:09:18 PDT)
yjlee
[AMBER] sudden and rapid configuration change in NVT simulation
(Fri May 30 2014 - 01:44:46 PDT)
zahra khatti
[AMBER] mmpbsa
(Thu May 22 2014 - 07:59:23 PDT)
张明焜
[AMBER] can “NAB: Molecular mechanics and dynamics” do qmmm caculation?
(Mon May 19 2014 - 01:59:42 PDT)
[AMBER] how to generate a complete amino acid in suitable for the vacuum simulation
(Tue May 06 2014 - 20:38:49 PDT)
[AMBER] Questions about nmode Command
(Sun May 04 2014 - 00:59:01 PDT)
王珍
Re: [AMBER] protonate question
(Sat May 31 2014 - 00:52:15 PDT)
[AMBER] protonate question
(Thu May 29 2014 - 17:45:24 PDT)
Re: [AMBER] 3NKB5
(Wed May 28 2014 - 18:17:00 PDT)
Re: [AMBER] 3NKB5
(Wed May 28 2014 - 07:56:49 PDT)
Re: [AMBER] 3NKB5
(Wed May 28 2014 - 07:19:11 PDT)
Re: [AMBER] 3NKB5
(Wed May 28 2014 - 06:00:20 PDT)
[AMBER] 3NKB5
(Tue May 27 2014 - 00:08:27 PDT)
Last message date
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Sat May 31 2014 - 12:30:02 PDT
Archived on
: Sun Nov 24 2024 - 05:55:09 PST
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