Amber Archive Jun 2018 by author
343 messages
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Starting
Thu May 31 2018 - 22:30:02 PDT,
Ending
Sat Jun 30 2018 - 06:00:02 PDT
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Aashish Bhatt
Re: [AMBER] Dimension Box visualization
(Tue Jun 05 2018 - 03:09:48 PDT)
ABEL Stephane
Re: [AMBER] high values of RMSD during the simulation of molecular dynamics between DNA and small molecule. Does anyone explain?
(Fri Jun 01 2018 - 07:35:54 PDT)
Abhilash J
Re: [AMBER] Initial configuration of ADP and ion simulation using AMBER.
(Wed Jun 13 2018 - 09:46:09 PDT)
Re: [AMBER] Initial configuration of ADP and ion simulation using AMBER.
(Tue Jun 05 2018 - 11:38:47 PDT)
Akash Deep Biswas
Re: [AMBER] high values of RMSD during the simulation of molecular dynamics between DNA and small molecule. Does anyone explain?
(Fri Jun 01 2018 - 18:57:10 PDT)
Andrea H. Kasun
Re: [AMBER] compatibility of graphic card and Amber
(Tue Jun 05 2018 - 07:12:49 PDT)
[AMBER] compatibility of graphic card and Amber
(Tue Jun 05 2018 - 02:25:06 PDT)
andreas.tosstorff.cup.uni-muenchen.de
Re: [AMBER] Conda Installation error
(Thu Jun 07 2018 - 00:42:21 PDT)
Re: [AMBER] Conda Installation error
(Wed Jun 06 2018 - 00:41:44 PDT)
anu chandra
[AMBER] Gaussian aMD in Amber14
(Fri Jun 29 2018 - 00:22:54 PDT)
Aravind Ravichandran
Re: [AMBER] Queries regarding bond command in leap
(Tue Jun 05 2018 - 22:43:43 PDT)
[AMBER] Queries regarding bond command in leap
(Tue Jun 05 2018 - 22:06:34 PDT)
[AMBER] NaN in NEB output
(Tue Jun 05 2018 - 21:41:51 PDT)
ATUL KUMAR
Re: [AMBER] Trajectory format
(Sat Jun 16 2018 - 11:26:29 PDT)
Re: [AMBER] Trajectory format
(Sat Jun 16 2018 - 07:36:45 PDT)
Re: [AMBER] Trajectory format
(Sat Jun 16 2018 - 07:23:07 PDT)
Re: [AMBER] Trajectory format
(Fri Jun 15 2018 - 22:09:29 PDT)
Re: [AMBER] Trajectory format
(Fri Jun 15 2018 - 22:00:39 PDT)
[AMBER] Trajectory format
(Fri Jun 15 2018 - 06:02:36 PDT)
Baptiste Legrand
Re: [AMBER] Using chirality restraints for modified residues
(Fri Jun 29 2018 - 02:43:44 PDT)
Re: [AMBER] Using chirality restraints for modified residues
(Fri Jun 29 2018 - 01:32:33 PDT)
[AMBER] Using chirality restraints for modified residues
(Thu Jun 28 2018 - 09:03:11 PDT)
BERGY
[AMBER] Amber16 + Ambertools17 + CUDA 9.0 + NVIDIA 390 Installation Guide
(Thu Jun 14 2018 - 10:10:17 PDT)
Berkant Düzgün
[AMBER] Amber14-GIST
(Thu Jun 21 2018 - 01:42:52 PDT)
Bill Ross
Re: [AMBER] Using chirality restraints for modified residues
(Fri Jun 29 2018 - 03:21:41 PDT)
Re: [AMBER] Using chirality restraints for modified residues
(Fri Jun 29 2018 - 01:52:44 PDT)
Re: [AMBER] why tleap adds TER in the middle of a DNA sequence
(Wed Jun 20 2018 - 19:05:40 PDT)
Re: [AMBER] Trajectory format
(Sat Jun 16 2018 - 07:56:23 PDT)
Re: [AMBER] Trajectory format
(Sat Jun 16 2018 - 07:31:26 PDT)
Re: [AMBER] Net salt ions ouside the solvent box after AddIons
(Thu Jun 14 2018 - 11:43:40 PDT)
Re: [AMBER] Charm-gui and water models
(Tue Jun 12 2018 - 13:28:34 PDT)
Re: [AMBER] water box with 64 molecules
(Sun Jun 10 2018 - 19:14:48 PDT)
Re: [AMBER] Distance restraint not working
(Fri Jun 08 2018 - 05:42:46 PDT)
Re: [AMBER] Distance restraint not working
(Fri Jun 08 2018 - 05:18:32 PDT)
Re: [AMBER] Distance restraint not working
(Fri Jun 08 2018 - 04:32:11 PDT)
Re: [AMBER] Queries regarding bond command in leap
(Tue Jun 05 2018 - 22:21:44 PDT)
Carlos Simmerling
Re: [AMBER] implicit solvent
(Fri Jun 29 2018 - 12:33:30 PDT)
Re: [AMBER] Using chirality restraints for modified residues
(Thu Jun 28 2018 - 09:15:21 PDT)
Re: [AMBER] Fwd: increase speed in amber using implcit solvent model
(Sun Jun 24 2018 - 04:18:56 PDT)
Re: [AMBER] NaN in NEB output
(Wed Jun 06 2018 - 05:20:37 PDT)
Re: [AMBER] compatibility of graphic card and Amber
(Tue Jun 05 2018 - 07:21:43 PDT)
Re: [AMBER] high values of RMSD during the simulation of molecular dynamics between DNA and small molecule. Does anyone explain?
(Sat Jun 02 2018 - 04:03:31 PDT)
Re: [AMBER] high values of RMSD during the simulation of molecular dynamics between DNA and small molecule. Does anyone explain?
(Fri Jun 01 2018 - 18:20:13 PDT)
Re: [AMBER] box size
(Fri Jun 01 2018 - 10:59:54 PDT)
Re: [AMBER] Calculation of the REMD exchange rate in amber 14
(Fri Jun 01 2018 - 08:17:26 PDT)
Re: [AMBER] high values of RMSD during the simulation of molecular dynamics between DNA and small molecule. Does anyone explain?
(Fri Jun 01 2018 - 08:17:01 PDT)
Re: [AMBER] high values of RMSD during the simulation of molecular dynamics between DNA and small molecule. Does anyone explain?
(Fri Jun 01 2018 - 07:33:14 PDT)
Charles Lin
Re: [AMBER] AMBER: targeted MD
(Thu Jun 21 2018 - 09:45:33 PDT)
Charles-Alexandre Mattelaer
Re: [AMBER] implicit solvent simmulation
(Sat Jun 30 2018 - 05:55:23 PDT)
Chetna Tyagi
[AMBER] Fwd: Accelerated MD re-weighting---- very high PMF values
(Mon Jun 11 2018 - 05:33:42 PDT)
Re: [AMBER] Accelerated MD re-weighting---- very high PMF values
(Sun Jun 03 2018 - 07:27:10 PDT)
[AMBER] Accelerated MD re-weighting---- very high PMF values
(Sun Jun 03 2018 - 07:25:54 PDT)
Chhaya Singh
Re: [AMBER] implicit solvent simmulation
(Fri Jun 29 2018 - 14:40:04 PDT)
Re: [AMBER] implicit solvent
(Fri Jun 29 2018 - 12:33:23 PDT)
Re: [AMBER] implicit solvent
(Fri Jun 29 2018 - 12:37:05 PDT)
Re: [AMBER] implicit solvent
(Fri Jun 29 2018 - 12:29:24 PDT)
[AMBER] implicit solvent simmulation
(Fri Jun 29 2018 - 12:26:24 PDT)
Re: [AMBER] implicit solvent
(Thu Jun 28 2018 - 11:42:31 PDT)
Re: [AMBER] implicit solvent
(Thu Jun 28 2018 - 11:28:40 PDT)
[AMBER] implicit solvent
(Thu Jun 28 2018 - 11:07:42 PDT)
Re: [AMBER] Fwd: increase speed in amber using implcit solvent model
(Wed Jun 27 2018 - 11:26:23 PDT)
Re: [AMBER] Fwd: increase speed in amber using implcit solvent model
(Sun Jun 24 2018 - 23:57:37 PDT)
Re: [AMBER] Fwd: increase speed in amber using implcit solvent model
(Sun Jun 24 2018 - 23:44:06 PDT)
[AMBER] Fwd: increase speed in amber using implcit solvent model
(Sun Jun 24 2018 - 00:26:33 PDT)
Chris Neale
Re: [AMBER] Initial configuration of ADP and ion simulation using AMBER.
(Sat Jun 02 2018 - 16:04:57 PDT)
Christopher Faulkner
[AMBER] Time averaged mean squared displacement
(Mon Jun 25 2018 - 08:50:34 PDT)
Re: [AMBER] Lipid diffusion COM drift
(Mon Jun 25 2018 - 04:39:27 PDT)
[AMBER] Lipid diffusion COM drift
(Fri Jun 22 2018 - 01:43:22 PDT)
Re: [AMBER] Simulating drug molecules in lipid bilayers
(Thu Jun 14 2018 - 02:36:37 PDT)
[AMBER] Simulating drug molecules in lipid bilayers
(Tue Jun 12 2018 - 05:29:47 PDT)
Cruzeiro,Vinicius Wilian D
Re: [AMBER] Problem regarding running independent parallel simulations in AMBER14 using -rem<#>
(Mon Jun 25 2018 - 08:48:17 PDT)
Re: [AMBER] Problem regarding running independent parallel simulations in AMBER14 using -rem<#>
(Mon Jun 25 2018 - 08:01:14 PDT)
Re: [AMBER] restarting REMD vacuum simulation with watercap
(Tue Jun 19 2018 - 13:43:54 PDT)
Danial Pourjafar-Dehkordi
Re: [AMBER] Charm-gui and water models
(Fri Jun 15 2018 - 06:02:41 PDT)
[AMBER] Charm-gui and water models
(Tue Jun 12 2018 - 08:56:10 PDT)
Daniel Roe
Re: [AMBER] Question on writing clustering information with cpptraj
(Tue Jun 26 2018 - 10:53:52 PDT)
Re: [AMBER] Question on writing clustering information with cpptraj
(Tue Jun 26 2018 - 06:35:29 PDT)
Re: [AMBER] How to "un-strip" the MG* atom from mmpbsa
(Wed Jun 20 2018 - 05:35:42 PDT)
Re: [AMBER] Reg. esander or energy command not found.
(Wed Jun 20 2018 - 05:32:21 PDT)
Re: [AMBER] Problems in running MMPBSA.py: undefined symbol: __libm_feature_flag
(Wed Jun 20 2018 - 05:28:01 PDT)
Re: [AMBER] GIST preparetion error
(Wed Jun 20 2018 - 05:25:36 PDT)
Re: [AMBER] Trajectory format
(Fri Jun 15 2018 - 09:54:28 PDT)
Re: [AMBER] CPPTRAJ H-bond Plot
(Mon Jun 11 2018 - 12:28:13 PDT)
Re: [AMBER] Change x-axis from frame # to time in gnu plot created with secstruct command using cpptraj
(Mon Jun 11 2018 - 12:20:21 PDT)
Re: [AMBER] Amber DSSP : Secondary structure
(Wed Jun 06 2018 - 10:07:01 PDT)
Re: [AMBER] how to calculate the mass center distance between adjacent repeat units of one polymer chain
(Tue Jun 05 2018 - 12:11:53 PDT)
Re: [AMBER] Radial distribution function of waters
(Tue Jun 05 2018 - 06:05:34 PDT)
Darrin York
Re: [AMBER] AMBER18 pmemd.cuda TI generates Error: an illegal memory access was encountered launching kernel kNLSkinTest
(Mon Jun 25 2018 - 11:00:24 PDT)
David A Case
Re: [AMBER] cpptraj and sander
(Fri Jun 29 2018 - 18:03:09 PDT)
Re: [AMBER] calculating force correlation in trajectory
(Thu Jun 28 2018 - 15:04:51 PDT)
Re: [AMBER] implicit solvent
(Thu Jun 28 2018 - 11:40:31 PDT)
Re: [AMBER] calculating force correlation in trajectory
(Thu Jun 28 2018 - 11:37:13 PDT)
Re: [AMBER] Using chirality restraints for modified residues
(Thu Jun 28 2018 - 11:31:13 PDT)
Re: [AMBER] Regarding the MPI error in parallel running of 3D-RISM
(Thu Jun 28 2018 - 11:26:17 PDT)
Re: [AMBER] query regarding the Amber 12 compatibility with RHEL upgraded versions
(Thu Jun 28 2018 - 03:51:08 PDT)
Re: [AMBER] Install problems fftw for AMBER16
(Wed Jun 27 2018 - 08:34:43 PDT)
Re: [AMBER] Amber16 (with AmberToos16) install problems.
(Mon Jun 25 2018 - 11:31:34 PDT)
Re: [AMBER] Fortran runtime error: Cannot write to file opened for READ
(Mon Jun 25 2018 - 04:59:02 PDT)
Re: [AMBER] Extract force for every atom in a 100ns MD run trajectory
(Sun Jun 24 2018 - 13:18:15 PDT)
Re: [AMBER] Unit 5 Error on OPEN:mdin on clustuer with pmemd.cuda
(Sun Jun 24 2018 - 11:54:01 PDT)
Re: [AMBER] Fwd: increase speed in amber using implcit solvent model
(Sun Jun 24 2018 - 11:49:08 PDT)
Re: [AMBER] Difference between frcmod and mdl parameters
(Fri Jun 22 2018 - 11:02:29 PDT)
Re: [AMBER] script for converting amber parameters into CNS file
(Fri Jun 22 2018 - 05:43:19 PDT)
Re: [AMBER] why tleap adds TER in the middle of a DNA sequence
(Fri Jun 22 2018 - 05:40:23 PDT)
Re: [AMBER] Implicit solvent TI calculations with soft core potentials
(Wed Jun 20 2018 - 04:07:07 PDT)
Re: [AMBER] Problems in running MMPBSA.py: undefined symbol: __libm_feature_flag
(Wed Jun 20 2018 - 04:05:11 PDT)
Re: [AMBER] Amber16 + Ambertools17 + CUDA 9.0 + NVIDIA 390 Installation Guide
(Wed Jun 20 2018 - 04:03:46 PDT)
Re: [AMBER] Reg. esander or energy command not found.
(Wed Jun 20 2018 - 03:58:36 PDT)
Re: [AMBER] Idea of equilibration in MD before production?
(Mon Jun 18 2018 - 05:48:08 PDT)
Re: [AMBER] MMGBSA error FATAL: NATOM mismatch in coord and topology files
(Fri Jun 15 2018 - 04:46:05 PDT)
Re: [AMBER] Net salt ions ouside the solvent box after AddIons
(Wed Jun 13 2018 - 13:10:01 PDT)
Re: [AMBER] AMBER performance degradation on CPU compared to GPU
(Wed Jun 13 2018 - 05:52:51 PDT)
Re: [AMBER] CPPTRAJ: Wildcards for the frames to extract
(Wed Jun 13 2018 - 05:37:18 PDT)
Re: [AMBER] NetCDF trajectories in lower precision
(Wed Jun 13 2018 - 05:35:14 PDT)
Re: [AMBER] Running QMMM on Iron Core enzyme
(Mon Jun 11 2018 - 05:08:25 PDT)
Re: [AMBER] TrajError: start frame (51021) > total frames (5000)
(Mon Jun 11 2018 - 05:03:49 PDT)
Re: [AMBER] water box with 64 molecules
(Mon Jun 11 2018 - 04:58:18 PDT)
Re: [AMBER] Amber18 and CUDA 9.2
(Sat Jun 09 2018 - 05:59:25 PDT)
Re: [AMBER] MM-GBSA for recptor-magnesium-ligand complex
(Thu Jun 07 2018 - 04:28:20 PDT)
Re: [AMBER] Carbon-nanotube topology construction
(Thu Jun 07 2018 - 04:24:14 PDT)
Re: [AMBER] Amber18 and CUDA 9.2
(Wed Jun 06 2018 - 05:15:20 PDT)
Re: [AMBER] Conda Installation error
(Wed Jun 06 2018 - 05:08:02 PDT)
Re: [AMBER] Installing GPU version Amber18
(Tue Jun 05 2018 - 04:45:16 PDT)
Re: [AMBER] make test error: make: *** [test.serial] Error 2
(Tue Jun 05 2018 - 04:39:39 PDT)
Re: [AMBER] Radial distribution function of waters
(Mon Jun 04 2018 - 12:24:35 PDT)
Re: [AMBER] Query regarding 3D-RISM output
(Mon Jun 04 2018 - 12:21:56 PDT)
Re: [AMBER] A question about force-field parameters for organic compounds related to the purchase of AMBER-Certified EXXACT machine
(Sun Jun 03 2018 - 09:21:23 PDT)
Re: [AMBER] box size
(Sat Jun 02 2018 - 05:39:08 PDT)
Re: [AMBER] Clarification on forming covalent linkages
(Fri Jun 01 2018 - 05:26:00 PDT)
David Cerutti
Re: [AMBER] AMBER18 pmemd.cuda TI generates Error: an illegal memory access was encountered launching kernel kNLSkinTest
(Sat Jun 23 2018 - 15:10:26 PDT)
Re: [AMBER] Multi GPU performance
(Fri Jun 22 2018 - 08:00:01 PDT)
Re: [AMBER] Multi GPU performance
(Fri Jun 22 2018 - 07:08:32 PDT)
Re: [AMBER] Problem in Membrane Simulation : water molecules are out of box
(Thu Jun 21 2018 - 07:41:18 PDT)
Re: [AMBER] Bonds across the periodic boundaries
(Thu Jun 07 2018 - 20:53:33 PDT)
Devashish_Das
[AMBER] Running QMMM on Iron Core enzyme
(Mon Jun 11 2018 - 02:59:41 PDT)
DHEERAJ CHITARA
[AMBER] Reg. esander or energy command not found.
(Wed Jun 20 2018 - 00:30:53 PDT)
Dickson, Callum
Re: [AMBER] Simulating drug molecules in lipid bilayers
(Wed Jun 13 2018 - 16:24:22 PDT)
diego.soler.uam.es
Re: [AMBER] Radial distribution function of waters
(Tue Jun 05 2018 - 05:53:00 PDT)
[AMBER] Radial distribution function of waters
(Mon Jun 04 2018 - 08:08:24 PDT)
Dmitry Suplatov
[AMBER] AMBER performance degradation on CPU compared to GPU
(Wed Jun 13 2018 - 02:46:00 PDT)
Dow Hurst
Re: [AMBER] Geforce GTX 1080Ti testing on Amber18/CUDA 9.2
(Fri Jun 29 2018 - 11:28:45 PDT)
Duy Tran Phuoc
[AMBER] restarting REMD vacuum simulation with watercap
(Mon Jun 18 2018 - 20:25:56 PDT)
Edjan Silva
Re: [AMBER] high values of RMSD during the simulation of molecular dynamics between DNA and small molecule. Does anyone explain?
(Fri Jun 01 2018 - 18:38:42 PDT)
Re: [AMBER] high values of RMSD during the simulation of molecular dynamics between DNA and small molecule. Does anyone explain?
(Fri Jun 01 2018 - 18:15:09 PDT)
[AMBER] high values of RMSD during the simulation of molecular dynamics between DNA and small molecule. Does anyone explain?
(Fri Jun 01 2018 - 07:26:20 PDT)
emanuele
[AMBER] Atom Mask in QMMM calculation
(Sun Jun 03 2018 - 13:29:48 PDT)
emanuele falbo
Re: [AMBER] radial distribution from center of mass of solute
(Mon Jun 25 2018 - 03:50:12 PDT)
Re: [AMBER] radial distribution from center of mass of solute
(Mon Jun 25 2018 - 03:29:22 PDT)
Re: [AMBER] Trajectory format
(Fri Jun 15 2018 - 06:16:28 PDT)
Re: [AMBER] QMMM problem
(Mon Jun 11 2018 - 07:34:50 PDT)
Re: [AMBER] Atom Mask in QMMM calculation
(Mon Jun 04 2018 - 02:31:48 PDT)
ersin gündeğer
Re: [AMBER] make test error: make: *** [test.serial] Error 2
(Thu Jun 07 2018 - 06:21:05 PDT)
[AMBER] make test error: make: *** [test.serial] Error 2
(Tue Jun 05 2018 - 00:41:32 PDT)
Facundo Gomes
[AMBER] Free Energy landscape (FEL)
(Mon Jun 11 2018 - 19:58:46 PDT)
Felipe Franco Gonzalez
Re: [AMBER] Installing GPU version Amber18
(Tue Jun 05 2018 - 06:46:47 PDT)
Feng Pan
Re: [AMBER] Periodic boundary conditions and N_OF_BONDS_COLVAR
(Tue Jun 12 2018 - 21:04:15 PDT)
Francesca Lønstad Bleken
[AMBER] QMMM interface for TURBOMOLE
(Mon Jun 25 2018 - 01:49:56 PDT)
FyD
Re: [AMBER] S-S bond
(Thu May 31 2018 - 22:22:31 PDT)
Gamze Özbay
Re: [AMBER] GIST preparetion error
(Thu Jun 21 2018 - 02:31:31 PDT)
[AMBER] GIST preparetion error
(Wed Jun 20 2018 - 05:19:19 PDT)
Garima Singh
Re: [AMBER] AMBER Digest, Vol 2314, Issue 1
(Thu Jun 07 2018 - 03:34:01 PDT)
[AMBER] Amber DSSP : Secondary structure
(Wed Jun 06 2018 - 04:17:18 PDT)
George M. Giambasu
Re: [AMBER] Regarding the MPI error in parallel running of 3D-RISM
(Fri Jun 29 2018 - 07:02:53 PDT)
Re: [AMBER] Regarding the MPI error in parallel running of 3D-RISM
(Thu Jun 28 2018 - 07:03:40 PDT)
Goetz, Andreas
Re: [AMBER] Atom Mask in QMMM calculation
(Sun Jun 03 2018 - 18:29:59 PDT)
Gustaf Olsson
Re: [AMBER] NetCDF trajectories in lower precision
(Wed Jun 13 2018 - 03:32:44 PDT)
Re: [AMBER] Radial distribution function of waters
(Tue Jun 05 2018 - 06:09:01 PDT)
Re: [AMBER] Radial distribution function of waters
(Mon Jun 04 2018 - 23:12:25 PDT)
Hai Nguyen
Re: [AMBER] Conda Installation error
(Wed Jun 06 2018 - 17:51:43 PDT)
Re: [AMBER] Using Pytraj to read and write velocity files
(Tue Jun 05 2018 - 21:21:08 PDT)
Re: [AMBER] Error in using pdb4amber command
(Sat Jun 02 2018 - 20:58:05 PDT)
Re: [AMBER] Using Pytraj to read and write velocity files
(Sat Jun 02 2018 - 15:44:59 PDT)
Holly Freedman
[AMBER] conversion of MG ions in parmed
(Thu Jun 07 2018 - 16:49:28 PDT)
Hugo Macdermott-Opeskin
[AMBER] Periodic boundary conditions and N_OF_BONDS_COLVAR
(Tue Jun 12 2018 - 18:51:01 PDT)
James Kress
Re: [AMBER] Multi GPU performance
(Fri Jun 22 2018 - 07:54:26 PDT)
Jason Ku Wang
[AMBER] Defining aMD Boost Parameters (Range and Distribution) for Hamiltonian Replica Exchange
(Mon Jun 18 2018 - 18:09:18 PDT)
Jason Swails
Re: [AMBER] psf from parmed
(Wed Jun 13 2018 - 19:38:19 PDT)
juan.franco.uam.es
[AMBER] Installing GPU version Amber18
(Tue Jun 05 2018 - 01:12:30 PDT)
Kasprzak, Wojciech (NIH/NCI) [C]
Re: [AMBER] Net salt ions - Thank you!
(Thu Jun 14 2018 - 13:10:19 PDT)
Re: [AMBER] Net salt ions ouside the solvent box after AddIons
(Wed Jun 13 2018 - 13:25:51 PDT)
Re: [AMBER] Net salt ions ouside the solvent box after AddIons
(Wed Jun 13 2018 - 12:53:27 PDT)
[AMBER] Net salt ions ouside the solvent box after AddIons
(Wed Jun 13 2018 - 12:11:55 PDT)
Kat G
[AMBER] why tleap adds TER in the middle of a DNA sequence
(Wed Jun 20 2018 - 11:40:52 PDT)
Kellon Belfon
Re: [AMBER] Extract force for every atom in a 100ns MD run trajectory
(Sun Jun 24 2018 - 17:58:33 PDT)
Kenneth Huang
[AMBER] Individual bridging water lifetimes by closest?
(Fri Jun 29 2018 - 12:21:19 PDT)
Korey M Reid
Re: [AMBER] Using Pytraj to read and write velocity files
(Wed Jun 06 2018 - 00:50:32 PDT)
Re: [AMBER] Using Pytraj to read and write velocity files
(Tue Jun 05 2018 - 21:03:40 PDT)
[AMBER] Using Pytraj to read and write velocity files
(Fri Jun 01 2018 - 21:08:03 PDT)
Krantzman, Kristin D
Re: [AMBER] Change x-axis from frame # to time in gnu plot created with secstruct command using cpptraj
(Mon Jun 11 2018 - 12:29:08 PDT)
[AMBER] Change x-axis from frame # to time in gnu plot created with secstruct command using cpptraj
(Mon Jun 11 2018 - 12:07:31 PDT)
[AMBER] change x-axis to time for gnuplot using cpptraj
(Thu Jun 07 2018 - 12:19:09 PDT)
Lachele Foley
Re: [AMBER] Converting atom naming to GLYCAM
(Tue Jun 05 2018 - 07:55:07 PDT)
Leena Aggarwal
Re: [AMBER] query regarding the Amber 12 compatibility with RHEL upgraded versions
(Thu Jun 28 2018 - 03:55:33 PDT)
[AMBER] query regarding the Amber 12 compatibility with RHEL upgraded versions
(Wed Jun 27 2018 - 23:50:17 PDT)
Re: [AMBER] rism1d query
(Wed Jun 27 2018 - 06:18:46 PDT)
Re: [AMBER] rism1d query
(Wed Jun 27 2018 - 05:30:25 PDT)
Re: [AMBER] rism1d query
(Wed Jun 27 2018 - 02:12:39 PDT)
Lei Zhao
[AMBER] protein sampling efficacy
(Tue Jun 05 2018 - 20:10:31 PDT)
Lod King
Re: [AMBER] calculating force correlation in trajectory
(Thu Jun 28 2018 - 16:30:06 PDT)
Re: [AMBER] calculating force correlation in trajectory
(Thu Jun 28 2018 - 11:47:14 PDT)
[AMBER] calculating force correlation in trajectory
(Thu Jun 28 2018 - 10:55:21 PDT)
Re: [AMBER] Fortran runtime error: Cannot write to file opened for READ
(Mon Jun 25 2018 - 09:02:57 PDT)
[AMBER] Fortran runtime error: Cannot write to file opened for READ
(Sun Jun 24 2018 - 22:33:39 PDT)
Re: [AMBER] Extract force for every atom in a 100ns MD run trajectory
(Sun Jun 24 2018 - 13:45:49 PDT)
[AMBER] Extract force for every atom in a 100ns MD run trajectory
(Sun Jun 24 2018 - 00:04:17 PDT)
Re: [AMBER] Amber16 + Ambertools17 + CUDA 9.0 + NVIDIA 390 Installation Guide
(Mon Jun 18 2018 - 19:03:25 PDT)
Markowska
Re: [AMBER] How to read .nc file in VMD
(Sun Jun 24 2018 - 05:14:51 PDT)
Re: [AMBER] NetCDF trajectories in lower precision
(Wed Jun 13 2018 - 03:41:52 PDT)
[AMBER] NetCDF trajectories in lower precision
(Wed Jun 13 2018 - 03:17:21 PDT)
Matias Machado
Re: [AMBER] Fwd: increase speed in amber using implcit solvent model
(Tue Jun 26 2018 - 09:27:58 PDT)
Re: [AMBER] Trajectory format
(Sat Jun 16 2018 - 11:13:19 PDT)
Re: [AMBER] Net salt ions ouside the solvent box after AddIons
(Thu Jun 14 2018 - 11:27:11 PDT)
Maximilian Ebert
Re: [AMBER] AMBER18 pmemd.cuda TI generates Error: an illegal memory access was encountered launching kernel kNLSkinTest
(Tue Jun 26 2018 - 13:50:20 PDT)
Re: [AMBER] AMBER18 pmemd.cuda TI generates Error: an illegal memory access was encountered launching kernel kNLSkinTest
(Sun Jun 24 2018 - 07:58:22 PDT)
[AMBER] AMBER18 pmemd.cuda TI generates Error: an illegal memory access was encountered launching kernel kNLSkinTest
(Sat Jun 23 2018 - 07:53:35 PDT)
Meng Wu
[AMBER] Unit 5 Error on OPEN:mdin on clustuer with pmemd.cuda
(Sun Jun 24 2018 - 02:23:11 PDT)
Midhun K Madhu
[AMBER] GaMD Not Running in GPU
(Tue Jun 12 2018 - 09:25:41 PDT)
Nikolay N. Kuzmich
[AMBER] Geforce GTX 1080Ti testing on Amber18/CUDA 9.2
(Fri Jun 29 2018 - 04:58:17 PDT)
Re: [AMBER] CPPTRAJ: Wildcards for the frames to extract
(Fri Jun 15 2018 - 08:15:01 PDT)
[AMBER] CPPTRAJ: Wildcards for the frames to extract
(Wed Jun 13 2018 - 05:12:19 PDT)
Re: [AMBER] Amber18 and CUDA 9.2
(Fri Jun 08 2018 - 04:53:00 PDT)
[AMBER] Amber18 and CUDA 9.2
(Wed Jun 06 2018 - 02:08:10 PDT)
Nuno Barbosa
[AMBER] REF_ENERGY in Titratable_residues.py
(Thu Jun 28 2018 - 06:52:35 PDT)
Parviz Seifpanahi Shabane
Re: [AMBER] Net salt ions ouside the solvent box after AddIons
(Wed Jun 13 2018 - 12:20:00 PDT)
Pengfei Li
Re: [AMBER] Including C4 terms LJ12-6-4
(Tue Jun 12 2018 - 13:11:51 PDT)
Re: [AMBER] psf from parmed
(Tue Jun 12 2018 - 13:02:01 PDT)
Re: [AMBER] Initial configuration of ADP and ion simulation using AMBER.
(Tue Jun 12 2018 - 12:52:30 PDT)
Re: [AMBER] Initial configuration of ADP and ion simulation using AMBER.
(Sat Jun 02 2018 - 15:07:44 PDT)
Re: [AMBER] problems with MCPY.py step 2
(Sat Jun 02 2018 - 11:58:52 PDT)
Pooria Farahani
Re: [AMBER] Including C4 terms LJ12-6-4
(Wed Jun 13 2018 - 04:00:52 PDT)
[AMBER] Including C4 terms LJ12-6-4
(Tue Jun 12 2018 - 05:41:53 PDT)
Portillo, Jennifer
[AMBER] cpptraj and sander
(Fri Jun 29 2018 - 07:15:05 PDT)
PRITI ROY
Re: [AMBER] Regarding the MPI error in parallel running of 3D-RISM
(Thu Jun 28 2018 - 21:52:02 PDT)
Re: [AMBER] Regarding the MPI error in parallel running of 3D-RISM
(Thu Jun 28 2018 - 10:49:24 PDT)
[AMBER] Regarding the MPI error in parallel running of 3D-RISM
(Thu Jun 28 2018 - 04:35:13 PDT)
Qing Lv
Re: [AMBER] How to read .nc file in VMD
(Sun Jun 24 2018 - 06:01:58 PDT)
[AMBER] How to read .nc file in VMD
(Sat Jun 23 2018 - 23:36:04 PDT)
Re: [AMBER] Problems in running MMPBSA.py: undefined symbol: __libm_feature_flag
(Fri Jun 22 2018 - 20:33:58 PDT)
[AMBER] Problems in running MMPBSA.py: undefined symbol: __libm_feature_flag
(Sun Jun 17 2018 - 21:56:07 PDT)
Qinghua Liao
Re: [AMBER] AMBER18 pmemd.cuda running error for divalent metal ions represented using multisite (dummy) atom model with the 12-6-4 LJ potential
(Tue Jun 26 2018 - 14:50:41 PDT)
Re: [AMBER] AMBER18 pmemd.cuda running error for divalent metal ions represented using multisite (dummy) atom model with the 12-6-4 LJ potential
(Thu Jun 21 2018 - 15:42:22 PDT)
[AMBER] direction in SMD
(Thu Jun 14 2018 - 06:59:19 PDT)
Re: [AMBER] box size
(Sat Jun 02 2018 - 05:46:33 PDT)
Re: [AMBER] box size
(Fri Jun 01 2018 - 11:12:40 PDT)
[AMBER] box size
(Fri Jun 01 2018 - 10:10:57 PDT)
Rakesh Srivastava
Re: [AMBER] rism1d convergence query
(Fri Jun 29 2018 - 00:36:11 PDT)
Re: [AMBER] rism1d convergence query
(Wed Jun 27 2018 - 23:02:32 PDT)
Re: [AMBER] rism1d query
(Wed Jun 27 2018 - 22:01:21 PDT)
Re: [AMBER] rism1d convergence query
(Wed Jun 27 2018 - 22:00:16 PDT)
Re: [AMBER] rism1d query
(Wed Jun 27 2018 - 05:37:21 PDT)
Re: [AMBER] rism1d query
(Wed Jun 27 2018 - 03:24:28 PDT)
[AMBER] rism1d convergence query
(Tue Jun 26 2018 - 23:14:17 PDT)
[AMBER] rism1d query
(Tue Jun 26 2018 - 22:34:22 PDT)
Re: [AMBER] Difference between frcmod and mdl parameters
(Fri Jun 22 2018 - 21:14:12 PDT)
[AMBER] Difference between frcmod and mdl parameters
(Fri Jun 22 2018 - 10:16:43 PDT)
Re: [AMBER] Query regarding 3D-RISM output
(Mon Jun 04 2018 - 21:51:02 PDT)
[AMBER] Query regarding 3D-RISM output
(Sun Jun 03 2018 - 23:45:39 PDT)
Rana Rehan Khalid
Re: [AMBER] Cpptraj h-bond
(Thu Jun 21 2018 - 08:05:55 PDT)
[AMBER] Cpptraj h-bond
(Wed Jun 20 2018 - 10:37:26 PDT)
[AMBER] CPPTRAJ H-bond Plot
(Thu Jun 07 2018 - 04:33:42 PDT)
Ray Luo
Re: [AMBER] Problems in running MMPBSA.py: undefined symbol: __libm_feature_flag
(Mon Jun 18 2018 - 10:07:32 PDT)
RITUPARNA
[AMBER] Calculation of the REMD exchange rate in amber 14
(Fri Jun 01 2018 - 08:04:03 PDT)
RITUPARNA ROY
Re: [AMBER] Problem regarding running independent parallel simulations in AMBER14 using -rem<#>
(Mon Jun 25 2018 - 08:43:52 PDT)
[AMBER] Problem regarding running independent parallel simulations in AMBER14 using -rem<#>
(Mon Jun 25 2018 - 07:56:07 PDT)
Rodrigo Galindo
Re: [AMBER] Trajectory format
(Sat Jun 16 2018 - 07:06:48 PDT)
Ross Walker
Re: [AMBER] compatibility of graphic card and Amber
(Wed Jun 06 2018 - 07:10:10 PDT)
Re: [AMBER] A question about force-field parameters for organic compounds related to the purchase of AMBER-Certified EXXACT machine
(Sun Jun 03 2018 - 10:02:23 PDT)
Re: [AMBER] Are 1070Ti GPUs Supported?
(Sun Jun 03 2018 - 05:05:35 PDT)
Ruth Helena Tichauer
[AMBER] lifetime analysis of native/nonnative contacts data
(Fri Jun 01 2018 - 04:28:46 PDT)
Seibold, Steve Allan
[AMBER] Install problems fftw for AMBER16
(Tue Jun 26 2018 - 11:10:22 PDT)
[AMBER] Amber16 (with AmberToos16) install problems.
(Mon Jun 25 2018 - 08:55:07 PDT)
senal dinuka
Re: [AMBER] Idea of equilibration in MD before production?
(Mon Jun 18 2018 - 08:53:16 PDT)
[AMBER] Idea of equilibration in MD before production?
(Sun Jun 17 2018 - 20:54:37 PDT)
[AMBER] Converting atom naming to GLYCAM
(Tue Jun 05 2018 - 01:50:11 PDT)
[AMBER] Clarification on forming covalent linkages
(Fri Jun 01 2018 - 02:00:35 PDT)
Shilpa Gupta
Re: [AMBER] radial distribution from center of mass of solute
(Mon Jun 25 2018 - 03:37:20 PDT)
[AMBER] radial distribution from center of mass of solute
(Mon Jun 25 2018 - 02:57:42 PDT)
Re: [AMBER] Carbon-nanotube topology construction
(Thu Jun 07 2018 - 06:04:32 PDT)
[AMBER] Carbon-nanotube topology construction
(Thu Jun 07 2018 - 02:44:10 PDT)
Shirin Jamshidi
[AMBER] Amber16 with AmberTools18
(Thu Jun 28 2018 - 02:13:53 PDT)
Simon Kit Sang Chu
Re: [AMBER] Distance restraint not working
(Mon Jun 11 2018 - 08:15:09 PDT)
Re: [AMBER] Distance restraint not working
(Sat Jun 09 2018 - 03:29:28 PDT)
Re: [AMBER] Distance restraint not working
(Fri Jun 08 2018 - 07:31:43 PDT)
Re: [AMBER] Distance restraint not working
(Fri Jun 08 2018 - 05:22:20 PDT)
Re: [AMBER] Distance restraint not working
(Fri Jun 08 2018 - 04:50:53 PDT)
[AMBER] Distance restraint not working
(Fri Jun 08 2018 - 04:13:07 PDT)
[AMBER] Advanced restraints in protein mutation
(Wed Jun 06 2018 - 02:21:10 PDT)
somdev pahari
[AMBER] Problem in Membrane Simulation : water molecules are out of box
(Thu Jun 21 2018 - 07:21:45 PDT)
Srinivasaraghavan KANNAN
[AMBER] Implicit solvent TI calculations with soft core potentials
(Mon Jun 18 2018 - 19:51:13 PDT)
[AMBER] Implicit solvent TI calculations with soft core potentials
(Sun Jun 17 2018 - 21:11:54 PDT)
Stefano Guglielmo
Re: [AMBER] psf from parmed
(Wed Jun 13 2018 - 23:59:29 PDT)
Re: [AMBER] psf from parmed
(Tue Jun 12 2018 - 13:33:53 PDT)
[AMBER] psf from parmed
(Thu Jun 07 2018 - 16:56:46 PDT)
Stephan Schott
Re: [AMBER] Lipid diffusion COM drift
(Mon Jun 25 2018 - 06:00:25 PDT)
Re: [AMBER] Lipid diffusion COM drift
(Fri Jun 22 2018 - 03:44:42 PDT)
Re: [AMBER] Deal with trajectoy PBC
(Fri Jun 15 2018 - 08:15:40 PDT)
Re: [AMBER] Distance restraint not working
(Mon Jun 11 2018 - 02:07:28 PDT)
Re: [AMBER] Error at runtime running AMBER18 with CUDA91 on GTX980
(Fri Jun 08 2018 - 11:07:36 PDT)
Re: [AMBER] Distance restraint not working
(Fri Jun 08 2018 - 10:16:59 PDT)
Re: [AMBER] Distance restraint not working
(Fri Jun 08 2018 - 04:40:13 PDT)
Re: [AMBER] Installing GPU version Amber18
(Tue Jun 05 2018 - 02:30:44 PDT)
Subha Kalyaanamoorthy
Re: [AMBER] Question on writing clustering information with cpptraj
(Tue Jun 26 2018 - 11:50:12 PDT)
Re: [AMBER] Question on writing clustering information with cpptraj
(Tue Jun 26 2018 - 10:29:58 PDT)
[AMBER] Question on writing clustering information with cpptraj
(Fri Jun 22 2018 - 11:04:30 PDT)
[AMBER] Question on writing clustering information
(Thu Jun 21 2018 - 17:57:31 PDT)
Thomas C Bishop
Re: [AMBER] Bonds across the periodic boundaries
(Fri Jun 08 2018 - 09:53:09 PDT)
Thomas Cheatham
Re: [AMBER] bad atom type for Mn after running mmpbsa
(Wed Jun 20 2018 - 03:53:35 PDT)
Re: [AMBER] How to "un-strip" the MG* atom from mmpbsa
(Wed Jun 20 2018 - 03:42:53 PDT)
Tom Kurtzman
Re: [AMBER] GIST preparetion error
(Thu Jun 21 2018 - 09:21:54 PDT)
Re: [AMBER] Amber14-GIST
(Thu Jun 21 2018 - 09:18:38 PDT)
Re: [AMBER] GIST preparetion error
(Wed Jun 20 2018 - 06:28:44 PDT)
Tyler Luchko (Lists)
Re: [AMBER] rism1d convergence query
(Thu Jun 28 2018 - 09:20:29 PDT)
Re: [AMBER] rism1d convergence query
(Wed Jun 27 2018 - 10:00:19 PDT)
Re: [AMBER] rism1d query
(Wed Jun 27 2018 - 09:52:09 PDT)
Urszula Uciechowska
[AMBER] script for converting amber parameters into CNS file
(Wed Jun 20 2018 - 04:31:00 PDT)
Re: [AMBER] How to "un-strip" the MG* atom from mmpbsa
(Wed Jun 20 2018 - 03:50:11 PDT)
[AMBER] bad atom type for Mn after running mmpbsa
(Wed Jun 20 2018 - 02:49:15 PDT)
[AMBER] How to "un-strip" the MG* atom from mmpbsa
(Wed Jun 20 2018 - 02:41:08 PDT)
[AMBER] Progress bar will not be used during Run [strip :WAT, Cl*, CIO, Cs+, IB, K*, Li+, MG*, Na+ ...]
(Tue Jun 19 2018 - 02:55:12 PDT)
[AMBER] MMGBSA error FATAL: NATOM mismatch in coord and topology files
(Thu Jun 14 2018 - 22:45:55 PDT)
Re: [AMBER] MM-GBSA for recptor-magnesium-ligand complex
(Wed Jun 13 2018 - 06:07:36 PDT)
[AMBER] MM-GBSA for recptor-magnesium-ligand complex
(Thu Jun 07 2018 - 03:24:23 PDT)
Wesley Michael Botello-Smith
Re: [AMBER] Deal with trajectoy PBC
(Fri Jun 15 2018 - 09:54:48 PDT)
Re: [AMBER] Error at runtime running AMBER18 with CUDA91 on GTX980
(Fri Jun 08 2018 - 11:30:47 PDT)
[AMBER] Error at runtime running AMBER18 with CUDA91 on GTX980
(Fri Jun 08 2018 - 10:36:54 PDT)
Re: [AMBER] how to calculate the mass center distance between adjacent repeat units of one polymer chain
(Tue Jun 05 2018 - 10:13:23 PDT)
Xiaoyu Wang
[AMBER] Bonds across the periodic boundaries
(Thu Jun 07 2018 - 20:32:57 PDT)
y-okabe.cc.miyakonojo-nct.ac.jp
Re: [AMBER] TrajError: start frame (51021) > total frames (5000)
(Mon Jun 11 2018 - 07:26:22 PDT)
Zachary Fallon
Re: [AMBER] compatibility of graphic card and Amber
(Tue Jun 05 2018 - 06:52:33 PDT)
Re: [AMBER] Are 1070Ti GPUs Supported?
(Sun Jun 03 2018 - 12:50:39 PDT)
[AMBER] Are 1070Ti GPUs Supported?
(Fri Jun 01 2018 - 09:24:16 PDT)
Zahra Khatti
[AMBER] Cuda
(Sat Jun 30 2018 - 05:47:33 PDT)
Zuo, Zhicheng
Re: [AMBER] AMBER18 pmemd.cuda running error for divalent metal ions represented using multisite (dummy) atom model with the 12-6-4 LJ potential
(Sat Jun 23 2018 - 07:51:11 PDT)
[AMBER] AMBER18 pmemd.cuda running error for divalent metal ions represented using multisite (dummy) atom model with the 12-6-4 LJ potential
(Thu Jun 21 2018 - 14:45:16 PDT)
唐元晖
Re: [AMBER] how to calculate the mass center distance between adjacent repeat units of one polymer chain
(Tue Jun 05 2018 - 13:09:17 PDT)
[AMBER] how to calculate the mass center distance between adjacent repeat units of one polymer chain
(Tue Jun 05 2018 - 09:53:49 PDT)
[AMBER] Question about how to calculate the mass center distance between adjacent repeat units of one polymer chain
(Fri Jun 01 2018 - 14:19:26 PDT)
岡部 勇二
[AMBER] TrajError: start frame (51021) > total frames (5000)
(Mon Jun 11 2018 - 00:52:22 PDT)
李耀
[AMBER] AMBER: targeted MD
(Tue Jun 19 2018 - 22:03:47 PDT)
赵东波
[AMBER] water box with 64 molecules
(Sun Jun 10 2018 - 18:22:47 PDT)
陈金峰
[AMBER] Multi GPU performance
(Fri Jun 22 2018 - 04:58:58 PDT)
[AMBER] Deal with trajectoy PBC
(Fri Jun 15 2018 - 06:59:39 PDT)
[AMBER] QMMM problem
(Mon Jun 11 2018 - 06:59:45 PDT)
Last message date
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Sat Jun 30 2018 - 06:00:02 PDT
Archived on
: Mon Nov 25 2024 - 05:55:34 PST
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