Amber Archive May 2013: by date

Wednesday, 1 May 2013
- Re: [AMBER] improper Dihedral Specification David A Case
- [AMBER] psf files from cellulose builder Rasha Alqus
- Re: [AMBER] DNA basestep stacking energy/interaction energy BERGY
- Re: [AMBER] improper Dihedral Specification Bill Ross
- [AMBER] restart a md simulation 纪晓峰
- [AMBER] restart a md simulation 纪晓峰
- [AMBER] occasional distortion of solute molecule crazylyf
- [AMBER] Amber 12 installation on GPU Shozeb Haider
Thursday, 2 May 2013
- Re: [AMBER] Amber 12 installation on GPU hannes.loeffler.stfc.ac.uk
- Re: [AMBER] restart a md simulation Anselm Horn
- [AMBER] cpptraj hbond: how to efficiently gather receptor-ligand hydrogen bonding statistics? Jan-Philip Gehrcke
- Re: [AMBER] Amber 12 installation on GPU David A Case
- Re: [AMBER] cpptraj hbond: how to efficiently gather receptor-ligand hydrogen bonding statistics? Daniel Roe
- Re: [AMBER] Amber 12 installation on GPU Ross Walker
- Re: [AMBER] cpptraj hbond: how to efficiently gather receptor-ligand hydrogen bonding statistics? Jan-Philip Gehrcke
- [AMBER] PM6 fails for DMSO system me, Nancy
- Re: [AMBER] PM6 fails for DMSO system Jason Swails
- Re: [AMBER] PM6 fails for DMSO system me, Nancy
Friday, 3 May 2013
- Re: [AMBER] MMPBSA.py: ECAVITY / ENPOLAR discrepancy Jan-Philip Gehrcke
- [AMBER] vlimit exceed followed by SHAKE failure seçkin Boz
- Re: [AMBER] vlimit exceed followed by SHAKE failure David A Case
- Re: [AMBER] vlimit exceed followed by SHAKE failure seçkin Boz
- Re: [AMBER] MMPBSA.py: ECAVITY / ENPOLAR discrepancy Jason Swails
- Re: [AMBER] MMPBSA.py: ECAVITY / ENPOLAR discrepancy Jan-Philip Gehrcke
- [AMBER] Advice on length of production simulation Chris Chris
- [AMBER] Need your help Poornima Iyer
- Re: [AMBER] Need your help David A Case
- Re: [AMBER] vlimit exceed followed by SHAKE failure David A Case
- Re: [AMBER] PM6 fails for DMSO system me, Nancy
Saturday, 4 May 2013
- [AMBER] MMPBSA Error: gb>0 is incompatible with periodic boundary conditions. Angelica Parente
- [AMBER] radial distribution function problem Jio M
- Re: [AMBER] Advice on length of production simulation Marc van der Kamp
- Re: [AMBER] MMPBSA Error: gb>0 is incompatible with periodic boundary conditions. Jan-Philip Gehrcke
- Re: [AMBER] radial distribution function problem Daniel Roe
- Re: [AMBER] MMPBSA Error: gb>0 is incompatible with periodic boundary conditions. David A Case
- [AMBER] Ambertools13 installation issue Chinthaka Ratnaweera
- Re: [AMBER] Ambertools13 installation issue Daniel Roe
- Re: [AMBER] MMPBSA Error: gb>0 is incompatible with periodic boundary conditions. Jason Swails
- Re: [AMBER] Ambertools13 installation issue Jason Swails
- Re: [AMBER] Ambertools13 installation issue Chinthaka Ratnaweera
- Re: [AMBER] Ambertools13 installation issue Hector A. Baldoni
- Re: [AMBER] PM6 fails for DMSO system Andreas Goetz
- Re: [AMBER] Ambertools13 installation issue Jason Swails
- Re: [AMBER] Ambertools13 installation issue Chinthaka Ratnaweera
- [AMBER] about halogen atom radius in MMPBSA calculation Wang Bo
- [AMBER] FW: Busco informacion sobre AMBER Patricia Castro Gutierrez
- Re: [AMBER] FW: Busco informacion sobre AMBER ros
- Re: [AMBER] FW: Busco informacion sobre AMBER Sergio R Aragon
Sunday, 5 May 2013
- Re: [AMBER] Ambertools13 installation issue Jason Swails
- [AMBER] I can't visualize (in vmd) the output from an Accelerated MD (aMD) run Jonathan Gough
- Re: [AMBER] Ambertools13 installation issue Chinthaka Ratnaweera
- [AMBER] problem in cpptraj installation Kshatresh Dutta Dubey
- Re: [AMBER] Ambertools13 installation issue Jason Swails
- Re: [AMBER] problem in cpptraj installation Daniel Roe
- Re: [AMBER] I can't visualize (in vmd) the output from an Accelerated MD (aMD) run Daniel Roe
- Re: [AMBER] problem in cpptraj installation Kshatresh Dutta Dubey
- Re: [AMBER] I can't visualize (in vmd) the output from an Accelerated MD (aMD) run Jonathan Gough
- Re: [AMBER] problem in cpptraj installation Daniel Roe
- Re: [AMBER] problem in cpptraj installation Kshatresh Dutta Dubey
- [AMBER] Fwd: Robin Jain
- Re: [AMBER] about halogen atom radius in MMPBSA calculation Nadine Homeyer
- [AMBER] Bug in cpptraj (AmberTools 13) Ake Sandgren
Monday, 6 May 2013
- [AMBER] Ptraj_segmentation fault KAMAKSHI SHARMA
- [AMBER] Protein-ligand docking kanika sharma
- Re: [AMBER] Protein-ligand docking David A Case
- Re: [AMBER] Ptraj_segmentation fault Jason Swails
- [AMBER] Test for NTP, ntt=3 Deák Robert
- Re: [AMBER] Test for NTP, ntt=3 Deák Robert
- [AMBER] MMPBSA.py error Le,Huy Tuan
- Re: [AMBER] MMPBSA.py error Jason Swails
- Re: [AMBER] Test for NTP, ntt=3 Jason Swails
- Re: [AMBER] MMPBSA.py error Le,Huy Tuan
- [AMBER] MMPBSA.py error Kshatresh Dutta Dubey
- Re: [AMBER] Bug in cpptraj (AmberTools 13) Daniel Roe
- [AMBER] mmpbsa error msg Chinthaka Ratnaweera
- Re: [AMBER] mmpbsa error msg Chinthaka Ratnaweera
- Re: [AMBER] problem in cpptraj installation Daniel Roe
- Re: [AMBER] problem in cpptraj installation Kshatresh Dutta Dubey
- [AMBER] the best APS is not zero, bonds involved by this atom are frozen Ashutosh Shandilya
- Re: [AMBER] MMPBSA.py error Chris Chris
- Re: [AMBER] MMPBSA.py error Kshatresh Dutta Dubey
- Re: [AMBER] the best APS is not zero, bonds involved by this atom are frozen Ashutosh Shandilya
- Re: [AMBER] problem in cpptraj installation Daniel Roe
- [AMBER] Open MPI failure David Winogradoff
- Re: [AMBER] Open MPI failure Daniel Roe
- Re: [AMBER] Open MPI failure David Winogradoff
- Re: [AMBER] Open MPI failure Ross Walker
- Re: [AMBER] MMPBSA.py error Jason Swails
- Re: [AMBER] mmpbsa error msg Jason Swails
- Re: [AMBER] mmpbsa error msg Chinthaka Ratnaweera
- Re: [AMBER] MMPBSA.py error Kshatresh Dutta Dubey
- Re: [AMBER] Open MPI failure David A Case
- Re: [AMBER] MMPBSA.py error Jason Swails
- Re: [AMBER] mmpbsa error msg Jason Swails
- Re: [AMBER] MMPBSA.py error Kshatresh Dutta Dubey
- Re: [AMBER] MMPBSA.py error Jason Swails
- [AMBER] Leap adding salt No solvent overlap Johannes Zuegg
- Re: [AMBER] Leap adding salt No solvent overlap Jason Swails
Tuesday, 7 May 2013
- [AMBER] Atom does not have a type. javier alejandro rendon carrillo
- Re: [AMBER] vlimit exceed followed by SHAKE failure seçkin Boz
- Re: [AMBER] Test for NTP, ntt=3 Deák Robert
- Re: [AMBER] Test for NTP, ntt=3 Deák Robert
- [AMBER] error while restart run Subrata Paul
- Re: [AMBER] Atom does not have a type. David A Case
- Re: [AMBER] error while restart run David A Case
- Re: [AMBER] vlimit exceed followed by SHAKE failure David A Case
- Re: [AMBER] Test for NTP, ntt=3 Jason Swails
- [AMBER] problems solvating Jonathan Gough
- [AMBER] Improper atom order Reinis Danne
- Re: [AMBER] problems solvating Daniel Roe
- Re: [AMBER] error while restart run Daniel Roe
- Re: [AMBER] Leap adding salt No solvent overlap Daniel Roe
- Re: [AMBER] Open MPI failure David Winogradoff
- [AMBER] PME and vdW cutoffs George Tzotzos
- [AMBER] Error in Membrane protein Simulation Dipankar Roy
- Re: [AMBER] Open MPI failure Daniel Roe
- Re: [AMBER] Open MPI failure David Winogradoff
- [AMBER] Optimal APBS parameters - Amber OR APBS defaults ? Marek Maly
- Re: [AMBER] PME and vdW cutoffs Andreas Goetz
- Re: [AMBER] Open MPI failure Daniel Roe
- [AMBER] when doing accelerated MD... Jonathan Gough
- Re: [AMBER] Optimal APBS parameters - Amber OR APBS defaults ? Ray Luo, Ph.D.
- Re: [AMBER] when doing accelerated MD... Jesper Sørensen
- Re: [AMBER] when doing accelerated MD... Jonathan Gough
- Re: [AMBER] Test for NTP, ntt=3 David A Case
- Re: [AMBER] Error in Membrane protein Simulation David A Case
- Re: [AMBER] Error in Membrane protein Simulation Ross Walker
- Re: [AMBER] Leap adding salt No solvent overlap Johannes Zuegg
- Re: [AMBER] Optimal APBS parameters - Amber OR APBS defaults ? Marek Maly
- [AMBER] How to average rst ? 赵媛
- [AMBER] Kind of RESTYPE setyanto md
Wednesday, 8 May 2013
- Re: [AMBER] Improper atom order Karl N. Kirschner
- [AMBER] ATTN: need revision seçkin Boz
- Re: [AMBER] Improper atom order Reinis Danne
- Re: [AMBER] ATTN: need revision Karl N. Kirschner
- [AMBER] unstable sytem-help Mary Varughese
- Re: [AMBER] Kind of RESTYPE David A Case
- [AMBER] Assistance required for MCPB program BALA SUBRAMANI G L
- [AMBER] fw: hey Wholly Peach
- Re: [AMBER] How to average rst ? Daniel Roe
- [AMBER] normal modes and intensity for raman spectrum Rasha Alqus
- [AMBER] pmemd performance on AMD 16cores x 4 (total 64 CPU cores) + 1 GPU sun
- Re: [AMBER] normal modes and intensity for raman spectrum Adrian Roitberg
- [AMBER] error running pmemd cuda tests Blake Mertz
- Re: [AMBER] pmemd performance on AMD 16cores x 4 (total 64 CPU cores) + 1 GPU Sergio R Aragon
- Re: [AMBER] error running pmemd cuda tests Jason Swails
- Re: [AMBER] pmemd performance on AMD 16cores x 4 (total 64 CPU cores) + 1 GPU Scott Le Grand
- Re: [AMBER] pmemd performance on AMD 16cores x 4 (total 64 CPU cores) + 1 GPU Ross Walker
- Re: [AMBER] Paper detailing GPU Simulations Compared to CPU code ET
- Re: [AMBER] Improper atom order Bill Ross
- Re: [AMBER] error running pmemd cuda tests Blake Mertz
- [AMBER] About free energy decomposition 赵媛
Thursday, 9 May 2013
- Re: [AMBER] error running pmemd cuda tests ET
- Re: [AMBER] Improper atom order Reinis Danne
- [AMBER] Fwd: unstable sytem-help Mary Varughese
- [AMBER] DNA ligand system broke up- help please Mary Varughese
- Re: [AMBER] vlimit exceed followed by SHAKE failure seçkin Boz
- Re: [AMBER] ATTN: need revision seçkin Boz
- [AMBER] AMBER GPU Cooling/usage Question ET
- Re: [AMBER] Fwd: unstable sytem-help David A Case
- [AMBER] how to create parameter file for Zn BALA SUBRAMANI G L
- Re: [AMBER] error running pmemd cuda tests Blake Mertz
- Re: [AMBER] AMBER GPU Cooling/usage Question Ross Walker
- Re: [AMBER] Fwd: unstable sytem-help Mary Varughese
- Re: [AMBER] error running pmemd cuda tests Jason Swails
- [AMBER] best way to get rmsd data between trajectory and DIFFERENT reference structure Andre C. Stiel
- [AMBER] Glass Transition Temperature Hector A. Baldoni
- Re: [AMBER] best way to get rmsd data between trajectory and DIFFERENT reference structure Daniel Roe
- [AMBER] apbsgrid error during sander.APBS calculation Marek Maly
- Re: [AMBER] apbsgrid error during sander.APBS calculation Robert Konecny
Friday, 10 May 2013
- Re: [AMBER] Fwd: unstable sytem-help David A Case
- [AMBER] Problem with the SMD aplication to proton transfer Santi Tolosa
- Re: [AMBER] best way to get rmsd data between trajectory and DIFFERENT reference structure Andre C. Stiel
- Re: [AMBER] apbsgrid error during sander.APBS calculation Marek Maly
- Re: [AMBER] best way to get rmsd data between trajectory and DIFFERENT reference structure Andre C. Stiel
- Re: [AMBER] best way to get rmsd data between trajectory and DIFFERENT reference structure Daniel Roe
- Re: [AMBER] best way to get rmsd data between trajectory and DIFFERENT reference structure Andre C. Stiel
- Re: [AMBER] Problem with the SMD aplication to proton transfer Brian Radak
- Re: [AMBER] best way to get rmsd data between trajectory and DIFFERENT reference structure Daniel Roe
- Re: [AMBER] Glass Transition Temperature David A Case
- Re: [AMBER] AMBER GPU Cooling/usage Question ET
- Re: [AMBER] error running pmemd cuda tests ET
- Re: [AMBER] Fwd: unstable sytem-help Mary Varughese
- Re: [AMBER] About free energy decomposition Bill Miller III
- [AMBER] drmsd Chris Chris
Saturday, 11 May 2013
- Re: [AMBER] drmsd Daniel Roe
- Re: [AMBER] Improper atom order Bill Ross
Sunday, 12 May 2013
- [AMBER] NaN from Mg2+ near ASP while running aMD Jonathan Gough
- Re: [AMBER] NaN from Mg2+ near ASP while running aMD Jonathan Gough
- [AMBER] sander.MPI is extremely slow Kshatresh Dutta Dubey
- [AMBER] MMPBSA.py Urszula Uciechowska
Monday, 13 May 2013
- Re: [AMBER] ATTN: need revision Karl N. Kirschner
- [AMBER] The force constants of bond and angle items are zero when the MCPB program reads the internal force constant matrix JiYuan Liu
- Re: [AMBER] sander.MPI is extremely slow Ross Walker
- [AMBER] Regarding mmpbsa.py dilrajl.bii.a-star.edu.sg
- Re: [AMBER] ATTN: need revision Karl N. Kirschner
- Re: [AMBER] Regarding mmpbsa.py David A Case
- Re: [AMBER] Regarding mmpbsa.py Jason Swails
- Re: [AMBER] MMPBSA.py Jason Swails
- [AMBER] Assistance required for capActivesite program Bala Subramani
- [AMBER] Inconsistent results for TI calculations Thomas Exner
- [AMBER] (nessun oggetto) Maurizio CELENTANO
- [AMBER] cpptraj strange warning with cluster command Miguel Ortiz Lombardía
- Re: [AMBER] cpptraj strange warning with cluster command Daniel Roe
- Re: [AMBER] (nessun oggetto) David A Case
- Re: [AMBER] cpptraj strange warning with cluster command Miguel Ortiz Lombardía
- Re: [AMBER] Inconsistent results for TI calculations steinbrt.rci.rutgers.edu
- Re: [AMBER] Inconsistent results for TI calculations Antonios Kolocouris
- Re: [AMBER] (nessun oggetto) Maurizio CELENTANO
- [AMBER] mpi4py installation error Kshatresh Dutta Dubey
- Re: [AMBER] mpi4py installation error Daniel Roe
- Re: [AMBER] mpi4py installation error Kshatresh Dutta Dubey
- Re: [AMBER] (nessun oggetto) David A Case
- [AMBER] amber tutorial A15 yanyuna
- Re: [AMBER] amber tutorial A15 David A Case
- Re: [AMBER] amber tutorial A15 yanyuna
- Re: [AMBER] amber tutorial A15 yanyuna
Tuesday, 14 May 2013
- [AMBER] assistance required for MTK++ BALA SUBRAMANI G L
Sunday, 12 May 2013
- [AMBER] error while using tleap with protein more than 248 residues sandeep singh
Tuesday, 14 May 2013
- [AMBER] Random Acceleration Molecular Dynamics (RAMD) Lars Skjærven
- Re: [AMBER] error while using tleap with protein more than 248 residues David A Case
- [AMBER] Nonpolar contribution in MMPBSA is very large Kshatresh Dutta Dubey
- Re: [AMBER] amber tutorial A15 David A Case
Monday, 13 May 2013
- [AMBER] Assistance required for capActivesite program BALA SUBRAMANI G L
Tuesday, 14 May 2013
- Re: [AMBER] Random Acceleration Molecular Dynamics (RAMD) Vlad Cojocaru
- [AMBER] random seed not in output file -> run not reproducible Jan-Philip Gehrcke
- Re: [AMBER] random seed not in output file -> run not reproducible Ross Walker
- Re: [AMBER] Assistance required for capActivesite program steinbrt.rci.rutgers.edu
- Re: [AMBER] random seed not in output file -> run not reproducible Jason Swails
- [AMBER] Free Energy for the G Quadruplex DNA including channel potassium ions Debayan Chakraborty
- Re: [AMBER] Nonpolar contribution in MMPBSA is very large Jason Swails
- Re: [AMBER] random seed not in output file -> run not reproducible Ross Walker
- Re: [AMBER] random seed not in output file -> run not reproducible Jan-Philip Gehrcke
- Re: [AMBER] random seed not in output file -> run not reproducible Jason Swails
- [AMBER] assistance required for bcl scripts BALA SUBRAMANI G L
- Re: [AMBER] Nonpolar contribution in MMPBSA is very large Kshatresh Dutta Dubey
- Re: [AMBER] Nonpolar contribution in MMPBSA is very large Jan-Philip Gehrcke
- Re: [AMBER] Nonpolar contribution in MMPBSA is very large Kshatresh Dutta Dubey
- [AMBER] SMD for proton transfer Santi Tolosa
- [AMBER] Problem with cpptraj vs ptraj imarcos
- Re: [AMBER] SMD for proton transfer M. L. Dodson
- [AMBER] preferred nucleic acids pbsa model Le,Huy Tuan
- Re: [AMBER] Problem with cpptraj vs ptraj Daniel Roe
- Re: [AMBER] Nonpolar contribution in MMPBSA is very large Jason Swails
- Re: [AMBER] Nonpolar contribution in MMPBSA is very large Kshatresh Dutta Dubey
- Re: [AMBER] error while using tleap with protein more than 248 residues Daniel Roe
- [AMBER] memory failure Jonathan Gough
- Re: [AMBER] memory failure Jonathan Gough
- Re: [AMBER] memory failure David A Case
- Re: [AMBER] memory failure Jonathan Gough
Wednesday, 15 May 2013
- [AMBER] assistance required for prep & frcmod file preparation BALA SUBRAMANI G L
- [AMBER] NAMD TO AMBER Rasha Alqus
- [AMBER] pmemd.CUDA installation problem Cenk \(Jenk\) Andac
- Re: [AMBER] pmemd.CUDA installation problem Jason Swails
- [AMBER] Interpreting .prmtop files David Winogradoff
- Re: [AMBER] Interpreting .prmtop files Hai Nguyen
- Re: [AMBER] Interpreting .prmtop files Jason Swails
- Re: [AMBER] pmemd.CUDA installation problem Cenk \(Jenk\) Andac
Thursday, 16 May 2013
- Re: [AMBER] pmemd.CUDA installation problem Cenk \(Jenk\) Andac
- [AMBER] SMD pulling GPU José Guilherme Vilhena Albuquerque d'Orey
- Re: [AMBER] SMD pulling GPU James Murdock
- Re: [AMBER] Problem with cpptraj vs ptraj imarcos
- [AMBER] References abou FF12SB Alan
- Re: [AMBER] Interpreting .prmtop files David Winogradoff
- Re: [AMBER] SMD pulling GPU Ross Walker
- Re: [AMBER] SMD pulling GPU José Guilherme Vilhena Albuquerque d'Orey
- Re: [AMBER] Interpreting .prmtop files David Winogradoff
- Re: [AMBER] Interpreting .prmtop files Jason Swails
- [AMBER] ff10 from amber11 maybe not using OL3?? Amparo Garcia Lopez
- Re: [AMBER] SMD pulling GPU Ross Walker
- Re: [AMBER] ff10 from amber11 maybe not using OL3?? Niel Henriksen
- Re: [AMBER] ff10 from amber11 maybe not using OL3?? pavel.banas.upol.cz
- Re: [AMBER] ff10 from amber11 maybe not using OL3?? Amparo Garcia Lopez
- [AMBER] How to dump distance information in the form of a vector file? Sajeewa Pemasinghe
- Re: [AMBER] ff10 from amber11 maybe not using OL3?? Amparo Garcia Lopez
- Re: [AMBER] How to dump distance information in the form of a vector file? Daniel Roe
- Re: [AMBER] ff10 from amber11 maybe not using OL3?? Ilyas Yildirim
- Re: [AMBER] How to dump distance information in the form of a vector file? Sajeewa Pemasinghe
- Re: [AMBER] How to dump distance information in the form of a vector file? Daniel Roe
- Re: [AMBER] ff10 from amber11 maybe not using OL3?? pavel.banas.upol.cz
- [AMBER] Parameters for Aluminum Ion Sun
Friday, 17 May 2013
- Re: [AMBER] ff10 from amber11 maybe not using OL3?? Amparo Garcia Lopez
- Re: [AMBER] ff10 from amber11 maybe not using OL3?? David A Case
- [AMBER] How to specify a vector to keep track of the velocities of all residues during a simulation? Sajeewa Pemasinghe
- Re: [AMBER] How to specify a vector to keep track of the velocities of all residues during a simulation? Daniel Roe
- Re: [AMBER] How to specify a vector to keep track of the velocities of all residues during a simulation? Sajeewa Pemasinghe
- [AMBER] force field parameters for acetylated lysine Senthil Natesan
- Re: [AMBER] How to specify a vector to keep track of the velocities of all residues during a simulation? David A Case
- [AMBER] Convergence criterion Anselm Horn
- Re: [AMBER] Convergence criterion David A Case
Saturday, 18 May 2013
- [AMBER] repeat MD simulations Kanin Wichapong
- Re: [AMBER] Convergence criterion Anselm Horn
- Re: [AMBER] repeat MD simulations Vlad Cojocaru
- [AMBER] MMPBSA for stability analysis Debayan Chakraborty
- Re: [AMBER] Convergence criterion Andreas Goetz
- Re: [AMBER] Convergence criterion Anselm Horn
- Re: [AMBER] MMPBSA for stability analysis Jason Swails
Sunday, 19 May 2013
- [AMBER] Grid command for water density BERGY
- [AMBER] antechamber and sqm problem Cenk \(Jenk\) Andac
- Re: [AMBER] antechamber and sqm problem Jason Swails
Monday, 20 May 2013
- [AMBER] Molecular Shape Searching on GPUs MARK
- Re: [AMBER] Molecular Shape Searching on GPUs MARK
- [AMBER] JAC benchmark tests on K20X Shan-ho Tsai
- Re: [AMBER] JAC benchmark tests on K20X Ross Walker
- Re: [AMBER] JAC benchmark tests on K20X Shan-ho Tsai
Tuesday, 21 May 2013
- Re: [AMBER] force field parameters for acetylated lysine Karl N. Kirschner
- [AMBER] rmsd vs rmsf nguyentb.bii.a-star.edu.sg
- [AMBER] Qm/mm gaussian template=1 jcgt
- [AMBER] cluster Mannan
- [AMBER] how to remove the overlap between molecules Rasha Alqus
- Re: [AMBER] rmsd vs rmsf Carlos Simmerling
- Re: [AMBER] JAC benchmark tests on K20X Jason Swails
- Re: [AMBER] rmsd vs rmsf Jason Swails
- Re: [AMBER] how to remove the overlap between molecules Jason Swails
- Re: [AMBER] Grid command for water density Jason Swails
- Re: [AMBER] References abou FF12SB Carlos Simmerling
- Re: [AMBER] rmsd vs rmsf nguyentb.bii.a-star.edu.sg
- [AMBER] problem with parmchk and a big organic molecule Rebeca García Fandiño
- Re: [AMBER] force field parameters for acetylated lysine Senthil Natesan
- Re: [AMBER] JAC benchmark tests on K20X Shan-ho Tsai
- Re: [AMBER] cluster Daniel Roe
- [AMBER] Energy and gradient inconsistent between AMBER and NAB Chris Whittleston
- Re: [AMBER] Energy and gradient inconsistent between AMBER and NAB Jason Swails
- [AMBER] cpptraj and avgcoord Anselm Horn
- Re: [AMBER] cpptraj and avgcoord Daniel Roe
- Re: [AMBER] Qm/mm gaussian template=1 Andreas Goetz
Wednesday, 22 May 2013
- Re: [AMBER] Qm/mm gaussian template=1 jcgt
- [AMBER] How to construct a mol2 file from a PDB and RESP output files ? ABEL Stephane 175950
- [AMBER] Energy and force blow up when I previously performe rmsd-fit for MD trajectory. kurisaki
- Re: [AMBER] How to construct a mol2 file from a PDB and RESP output files ? Ayesha Fatima
- [AMBER] pairwise decomposition using mmpbsa.py dilrajl.bii.a-star.edu.sg
- Re: [AMBER] pairwise decomposition using mmpbsa.py Jason Swails
- [AMBER] RE : How to construct a mol2 file from a PDB and RESP output files ? ABEL Stephane 175950
- Re: [AMBER] Energy and force blow up when I previously performe rmsd-fit for MD trajectory. Daniel Roe
- [AMBER] AMBERTOOLS: sqm fails to read input with more than 1000 external charges Franz Symalla
- Re: [AMBER] How to construct a mol2 file from a PDB and RESP output files ? David A Case
- Re: [AMBER] Energy and force blow up when I previously performe rmsd-fit for MD trajectory. kurisaki
- [AMBER] create prmtop strcuture file for sumoylated residues crazylyf
- [AMBER] RE : How to construct a mol2 file from a PDB and RESP output files ? ABEL Stephane 175950
- [AMBER] TR : [PROVENANCE INTERNET] RE : How to construct a mol2 file from a PDB and RESP outputfiles ? ABEL Stephane 175950
- Re: [AMBER] cpptraj and avgcoord Anselm Horn
- Re: [AMBER] RE : How to construct a mol2 file from a PDB and RESP output files ? Ayesha Fatima
- [AMBER] Query regarding mechanical unfolding of protein Manish Paul
- [AMBER] Relationship of time-autocorrelation plots for two lengths of time Sajeewa Pemasinghe
- Re: [AMBER] Relationship of time-autocorrelation plots for two lengths of time George Giambasu
- Re: [AMBER] AMBERTOOLS: sqm fails to read input with more than 1000 external charges Andreas Goetz
- Re: [AMBER] Relationship of time-autocorrelation plots for two lengths of time Sajeewa Pemasinghe
- [AMBER] Question about the normalization of velocity autocorrelation function Sajeewa Pemasinghe
Thursday, 23 May 2013
- Re: [AMBER] Qm/mm gaussian template=1 jcgt
- Re: [AMBER] AMBERTOOLS: sqm fails to read input with more than 1000 external charges Franz Symalla
- Re: [AMBER] How to construct a mol2 file from a PDB and RESP output files ? FyD
- [AMBER] RE : How to construct a mol2 file from a PDB and RESP output files ? ABEL Stephane 175950
- Re: [AMBER] Question about the normalization of velocity autocorrelation function David A Case
- Re: [AMBER] RE : How to construct a mol2 file from a PDB and RESP output files ? FyD
- Re: [AMBER] Question about the normalization of velocity autocorrelation function Sajeewa Pemasinghe
- [AMBER] Problem in updating AmberTools 12 Kshatresh Dutta Dubey
- Re: [AMBER] Relationship of time-autocorrelation plots for two lengths of time George Giambasu
- Re: [AMBER] Qm/mm gaussian template=1 Andreas Goetz
- [AMBER] example karplus.txt file for cpptraj jcoupling command Duggan, Brendan
- [AMBER] GPU version availability on Gordon-SDSC and Kraken NICS Senthil Natesan
- Re: [AMBER] GPU version availability on Gordon-SDSC and Kraken NICS Ross Walker
- [AMBER] TI erro - atom coordinate disagreement Kumar Sonu
- Re: [AMBER] TI erro - atom coordinate disagreement steinbrt.rci.rutgers.edu
- Re: [AMBER] example karplus.txt file for cpptraj jcoupling command Daniel Roe
- Re: [AMBER] Relationship of time-autocorrelation plots for two lengths of time Sajeewa Pemasinghe
- [AMBER] SQM: How to extract the charge density of sqm runs? Franz Symalla
- Re: [AMBER] Problem in updating AmberTools 12 Jason Swails
- [AMBER] Seg Fault in antechamber while writing ANTECHAMBER_AM1BCC_PRE.AC Jacob Monroe
- Re: [AMBER] RE : How to construct a mol2 file from a PDB and RESP output files ? Ayesha Fatima
- Re: [AMBER] Seg Fault in antechamber while writing ANTECHAMBER_AM1BCC_PRE.AC FyD
Friday, 24 May 2013
- Re: [AMBER] Seg Fault in antechamber while writing ANTECHAMBER_AM1BCC_PRE.AC David A Case
- Re: [AMBER] SQM: How to extract the charge density of sqm runs? David A Case
- [AMBER] About addIonsRand Marc van der Kamp
- [AMBER] Steered Molecular dynamics Santi Tolosa
- Re: [AMBER] Seg Fault in antechamber while writing ANTECHAMBER_AM1BCC_PRE.AC Jacob Monroe
- Re: [AMBER] example karplus.txt file for cpptraj jcoupling command Duggan, Brendan
- Re: [AMBER] example karplus.txt file for cpptraj jcoupling command Daniel Roe
- Re: [AMBER] SQM: How to extract the charge density of sqm runs? Andreas Goetz
Saturday, 25 May 2013
- Re: [AMBER] Seg Fault in antechamber while writing ANTECHAMBER_AM1BCC_PRE.AC David A Case
- Re: [AMBER] Seg Fault in antechamber while writing ANTECHAMBER_AM1BCC_PRE.AC FyD
- [AMBER] problem on compiling sander me, Nancy
Sunday, 26 May 2013
- [AMBER] Chained AMBER jobs crash on Dual GPU compute node. ET
- Re: [AMBER] Chained AMBER jobs crash on Dual GPU compute node. Jan-Philip Gehrcke
- Re: [AMBER] problem on compiling sander David A Case
Monday, 27 May 2013
- Re: [AMBER] Chained AMBER jobs crash on Dual GPU compute node. ET
- Re: [AMBER] Chained AMBER jobs crash on Dual GPU compute node. Jan-Philip Gehrcke
- Re: [AMBER] Seg Fault in antechamber while writing ANTECHAMBER_AM1BCC_PRE.AC Jacob Monroe
- Re: [AMBER] problem on compiling sander me, Nancy
- [AMBER] experiences with EVGA GTX TITAN Superclocked - memtestG80 - UNDERclocking in Linux ? Marek Maly
- [AMBER] atomicfluct George Tzotzos
- Re: [AMBER] atomicfluct Daniel Roe
- Re: [AMBER] atomicfluct George Tzotzos
- [AMBER] Free energy calculation of pyridine Bishnu Thapa
- Re: [AMBER] experiences with EVGA GTX TITAN Superclocked - memtestG80 - UNDERclocking in Linux ? Scott Le Grand
- Re: [AMBER] experiences with EVGA GTX TITAN Superclocked - memtestG80 - UNDERclocking in Linux ? Marek Maly
- Re: [AMBER] Free energy calculation of pyridine David A Case
Tuesday, 28 May 2013
- [AMBER] About water flags running parm7 with NAMD Francesco Pietra
- Re: [AMBER] About water flags running parm7 with NAMD Daniel Sindhikara
- Re: [AMBER] Chained AMBER jobs crash on Dual GPU compute node. ET
- [AMBER] RMSD calculation between trajectories dilrajl.bii.a-star.edu.sg
- Re: [AMBER] RMSD calculation between trajectories Niel Henriksen
- Re: [AMBER] RMSD calculation between trajectories Niel Henriksen
- [AMBER] Cpptraj and hbonds Fernando Martín García
- Re: [AMBER] RMSD calculation between trajectories Daniel Roe
- Re: [AMBER] About water flags running parm7 with NAMD Francesco Pietra
- Re: [AMBER] Cpptraj and hbonds Daniel Roe
- Re: [AMBER] Cpptraj and hbonds Fernando Martín García
- Re: [AMBER] About water flags running parm7 with NAMD Jason Swails
- Re: [AMBER] Cpptraj and hbonds Miguel Ortiz Lombardía
- Re: [AMBER] experiences with EVGA GTX TITAN Superclocked - memtestG80 - UNDERclocking in Linux ? Scott Le Grand
- Re: [AMBER] experiences with EVGA GTX TITAN Superclocked - memtestG80 - UNDERclocking in Linux ? Robert Konecny
- Re: [AMBER] Cpptraj and hbonds Daniel Roe
- Re: [AMBER] About water flags running parm7 with NAMD George Giambasu
- Re: [AMBER] atomicfluct Daniel Roe
- Re: [AMBER] About water flags running parm7 with NAMD Francesco Pietra
- Re: [AMBER] Interpreting .prmtop files David Winogradoff
- Re: [AMBER] experiences with EVGA GTX TITAN Superclocked - memtestG80 - UNDERclocking in Linux ? Gould, Ian R
- Re: [AMBER] experiences with EVGA GTX TITAN Superclocked - memtestG80 - UNDERclocking in Linux ? Scott Le Grand
- Re: [AMBER] Cpptraj and hbonds Miguel Ortiz Lombardía
- Re: [AMBER] atomicfluct David A Case
- [AMBER] GTX780 Fabrício Bracht
- Re: [AMBER] GTX780 Scott Le Grand
- Re: [AMBER] experiences with EVGA GTX TITAN Superclocked - memtestG80 - UNDERclocking in Linux ? ET
- Re: [AMBER] experiences with EVGA GTX TITAN Superclocked - memtestG80 - UNDERclocking in Linux ? Scott Le Grand
- [AMBER] Steered MD | Pulling Distance (between r2 and r2a in dist.RST file) is limitted to 100A | Offending restraint Emmanuel
- Re: [AMBER] Steered MD | Pulling Distance (between r2 and r2a in dist.RST file) is limitted to 100A | Offending restraint Adrian Roitberg
- Re: [AMBER] experiences with EVGA GTX TITAN Superclocked - memtestG80 - UNDERclocking in Linux ? Marek Maly
- Re: [AMBER] experiences with EVGA GTX TITAN Superclocked - memtestG80 - UNDERclocking in Linux ? Scott Le Grand
- Re: [AMBER] experiences with EVGA GTX TITAN Superclocked - memtestG80 - UNDERclocking in Linux ? Robert Konecny
- Re: [AMBER] experiences with EVGA GTX TITAN Superclocked - memtestG80 - UNDERclocking in Linux ? Marek Maly
- Re: [AMBER] experiences with EVGA GTX TITAN Superclocked - memtestG80 - UNDERclocking in Linux ? Scott Le Grand
- Re: [AMBER] experiences with EVGA GTX TITAN Superclocked - memtestG80 - UNDERclocking in Linux ? ET
- Re: [AMBER] experiences with EVGA GTX TITAN Superclocked - memtestG80 - UNDERclocking in Linux ? Divi/GMAIL
- Re: [AMBER] experiences with EVGA GTX TITAN Superclocked - memtestG80 - UNDERclocking in Linux ? ET
- Re: [AMBER] experiences with EVGA GTX TITAN Superclocked - memtestG80 - UNDERclocking in Linux ? Scott Le Grand
- Re: [AMBER] Steered MD | Pulling Distance (between r2 and r2a in dist.RST file) is limitted to 100A | Offending restraint David A Case
- Re: [AMBER] experiences with EVGA GTX TITAN Superclocked - memtestG80 - UNDERclocking in Linux ? Ross Walker
Wednesday, 29 May 2013
- Re: [AMBER] RMSD calculation between trajectories dilrajl.bii.a-star.edu.sg
- Re: [AMBER] RMSD calculation between trajectories Daniel Roe
- Re: [AMBER] Chained AMBER jobs crash on Dual GPU compute node. Jason Swails
- Re: [AMBER] Chained AMBER jobs crash on Dual GPU compute node. ET
- Re: [AMBER] Chained AMBER jobs crash on Dual GPU compute node. Jason Swails
- Re: [AMBER] experiences with EVGA GTX TITAN Superclocked - memtestG80 - UNDERclocking in Linux ? Marek Maly
- Re: [AMBER] experiences with EVGA GTX TITAN Superclocked - memtestG80 - UNDERclocking in Linux ? Scott Le Grand
- Re: [AMBER] experiences with EVGA GTX TITAN Superclocked - memtestG80 - UNDERclocking in Linux ? Jason Swails
- Re: [AMBER] experiences with EVGA GTX TITAN Superclocked - memtestG80 - UNDERclocking in Linux ? Scott Le Grand
- Re: [AMBER] experiences with EVGA GTX TITAN Superclocked - memtestG80 - UNDERclocking in Linux ? Marek Maly
- Re: [AMBER] experiences with EVGA GTX TITAN Superclocked - memtestG80 - UNDERclocking in Linux ? Marek Maly
- Re: [AMBER] experiences with EVGA GTX TITAN Superclocked - memtestG80 - UNDERclocking in Linux ? Scott Le Grand
- Re: [AMBER] experiences with EVGA GTX TITAN Superclocked - memtestG80 - UNDERclocking in Linux ? Marek Maly
- Re: [AMBER] experiences with EVGA GTX TITAN Superclocked - memtestG80 - UNDERclocking in Linux ? Scott Le Grand
- Re: [AMBER] experiences with EVGA GTX TITAN Superclocked - memtestG80 - UNDERclocking in Linux ? Marek Maly
- Re: [AMBER] experiences with EVGA GTX TITAN Superclocked - memtestG80 - UNDERclocking in Linux ? Jason Swails
Thursday, 30 May 2013
- Re: [AMBER] experiences with EVGA GTX TITAN Superclocked - memtestG80 - UNDERclocking in Linux ? ET
- Re: [AMBER] Chained AMBER jobs crash on Dual GPU compute node. ET
- Re: [AMBER] experiences with EVGA GTX TITAN Superclocked - memtestG80 - UNDERclocking in Linux ? ET
- Re: [AMBER] RMSD calculation between trajectories dilrajl.bii.a-star.edu.sg
- Re: [AMBER] experiences with EVGA GTX TITAN Superclocked - memtestG80 - UNDERclocking in Linux ? Marek Maly
- Re: [AMBER] experiences with EVGA GTX TITAN Superclocked - memtestG80 - UNDERclocking in Linux ? Marek Maly
- Re: [AMBER] RMSD calculation between trajectories Daniel Roe
- Re: [AMBER] experiences with EVGA GTX TITAN Superclocked - memtestG80 - UNDERclocking in Linux ? ET
- Re: [AMBER] experiences with EVGA GTX TITAN Superclocked - memtestG80 - UNDERclocking in Linux ? Marek Maly
- Re: [AMBER] experiences with EVGA GTX TITAN Superclocked - memtestG80 - UNDERclocking in Linux ? Scott Le Grand
- Re: [AMBER] experiences with EVGA GTX TITAN Superclocked - memtestG80 - UNDERclocking in Linux ? ET
- Re: [AMBER] experiences with EVGA GTX TITAN Superclocked - memtestG80 - UNDERclocking in Linux ? pavel.banas.upol.cz
- Re: [AMBER] experiences with EVGA GTX TITAN Superclocked - memtestG80 - UNDERclocking in Linux ? Scott Le Grand
- Re: [AMBER] experiences with EVGA GTX TITAN Superclocked - memtestG80 - UNDERclocking in Linux ? filip fratev
- Re: [AMBER] experiences with EVGA GTX TITAN Superclocked - memtestG80 - UNDERclocking in Linux ? Jason Swails
- Re: [AMBER] experiences with EVGA GTX TITAN Superclocked - memtestG80 - UNDERclocking in Linux ? Scott Le Grand
- Re: [AMBER] experiences with EVGA GTX TITAN Superclocked - memtestG80 - UNDERclocking in Linux ? Scott Le Grand
- [AMBER] Sample LMOD program (nab section of AmberTools manual) Chris Moth
- Re: [AMBER] experiences with EVGA GTX TITAN Superclocked - memtestG80 - UNDERclocking in Linux ? Marek Maly
- Re: [AMBER] experiences with EVGA GTX TITAN Superclocked - memtestG80 - UNDERclocking in Linux ? Scott Le Grand
- Re: [AMBER] experiences with EVGA GTX TITAN Superclocked - memtestG80 - UNDERclocking in Linux ? Marek Maly
- [AMBER] Error message when using mpirun on amber12_parallel 肖立
- Re: [AMBER] Error message when using mpirun on amber12_parallel Jason Swails
- Re: [AMBER] Error message when using mpirun on amber12_parallel 肖立
- Re: [AMBER] Error message when using mpirun on amber12_parallel Mandal, Sanat
- [AMBER] FW: Trouble generating topology files Teo, Theodosia Hua Swan - teohy004
- Re: [AMBER] Error message when using mpirun on amber12_parallel Jason Swails
- Re: [AMBER] Error message when using mpirun on amber12_parallel 肖立
Friday, 31 May 2013
- [AMBER] SMD calculation Santi Tolosa
- Re: [AMBER] experiences with EVGA GTX TITAN Superclocked - memtestG80 - UNDERclocking in Linux ? ET
- Re: [AMBER] experiences with EVGA GTX TITAN Superclocked - memtestG80 - UNDERclocking in Linux ? ET
- [AMBER] reference group and pulled group in umbrella sampling Jio M
- Re: [AMBER] experiences with EVGA GTX TITAN Superclocked - memtestG80 - UNDERclocking in Linux ? Marek Maly
- Re: [AMBER] AmberTools vs Amber David A Case
- Re: [AMBER] FW: Trouble generating topology files David A Case
- [AMBER] by pmemd.cuda runs Cenk \(Jenk\) Andac
- Re: [AMBER] experiences with EVGA GTX TITAN Superclocked - memtestG80 - UNDERclocking in Linux ? Marek Maly
- Re: [AMBER] by pmemd.cuda runs Marc van der Kamp
- [AMBER] hbond in ptraj and cpptraj pmaj.nencki.gov.pl
- Re: [AMBER] AmberTools vs Amber Mandal, Sanat
- Re: [AMBER] hbond in ptraj and cpptraj Daniel Roe
- Re: [AMBER] SMD calculation Jason Swails
- Re: [AMBER] by pmemd.cuda runs Daniel Roe
- Re: [AMBER] experiences with EVGA GTX TITAN Superclocked - memtestG80 - UNDERclocking in Linux ? filip fratev
- Re: [AMBER] experiences with EVGA GTX TITAN Superclocked - memtestG80 - UNDERclocking in Linux ? Marek Maly
- Re: [AMBER] experiences with EVGA GTX TITAN Superclocked - memtestG80 - UNDERclocking in Linux ? Marek Maly
- Re: [AMBER] by pmemd.cuda runs Moth, Chris
- Re: [AMBER] experiences with EVGA GTX TITAN Superclocked - memtestG80 - UNDERclocking in Linux ? ET
- Re: [AMBER] by pmemd.cuda runs Jason Swails
- Re: [AMBER] experiences with EVGA GTX TITAN Superclocked - memtestG80 - UNDERclocking in Linux ? Marek Maly
- Re: [AMBER] experiences with EVGA GTX TITAN Superclocked - memtestG80 - UNDERclocking in Linux ? ET
- Re: [AMBER] experiences with EVGA GTX TITAN Superclocked - memtestG80 - UNDERclocking in Linux ? Marek Maly
- Re: [AMBER] example karplus.txt file for cpptraj jcoupling command Duggan, Brendan
- Re: [AMBER] example karplus.txt file for cpptraj jcoupling command Daniel Roe
- Re: [AMBER] experiences with EVGA GTX TITAN Superclocked - memtestG80 - UNDERclocking in Linux ? ET

Last message date: Fri May 31 2013 - 16:00:02 PDT
Archived on: Wed Apr 17 2024 - 05:54:39 PDT

Amber Archive May 2013 by date