Amber Archive Aug 2012: by date

Tuesday, 31 July 2012
- [AMBER] cpptraj: autoimage + anchor works very well. Catein Catherine
- [AMBER] how to include derived charges in AMBER Sanjib Paul
Wednesday, 1 August 2012
- [AMBER] laptop GPU support Thomas Evangelidis
- [AMBER] AMBER on GPU: What is the maximum no. of nodes tested? Catein Catherine
- Re: [AMBER] laptop GPU support Jason Swails
- [AMBER] Problem in Amber12 and Amber12tools parallel installation in mac OS X 10.5 Prabu Manoharan
- Re: [AMBER] Problem in Amber12 and Amber12tools parallel installation in mac OS X 10.5 Jason Swails
- Re: [AMBER] Problem in Amber12 and Amber12tools parallel installation in mac OS X 10.5 David A Case
- [AMBER] receptor nmode calculation using amber12 mmpbsa.pl manikanthan bhavaraju
- Re: [AMBER] receptor nmode calculation using amber12 mmpbsa.pl Jason Swails
- Re: [AMBER] laptop GPU support Benjamin D Madej
- [AMBER] non polar solvation energy kirtana S
- [AMBER] large difference between MMGBSA and MMPBSA free energy Kong, Ren
- Re: [AMBER] large difference between MMGBSA and MMPBSA free energy Ray Luo, Ph.D.
- [AMBER] frcmod and lib files fro Cadmium Mahendra B Thapa
- Re: [AMBER] frcmod and lib files fro Cadmium Kong, Ren
- Re: [AMBER] large difference between MMGBSA and MMPBSA free energy Kong, Ren
- Re: [AMBER] FW: problem in converting rst-file to pdb using cpptraj Mahendra B Thapa
- Re: [AMBER] large difference between MMGBSA and MMPBSA free energy Ray Luo, Ph.D.
Thursday, 2 August 2012
- [AMBER] make test query vaibhav dixit
- Re: [AMBER] Making a complex Saaz Sakrikar
- [AMBER] Restarting PMEMD calculation after server shutdown Saaz Sakrikar
- Re: [AMBER] Making a complex David A Case
- Re: [AMBER] Restarting PMEMD calculation after server shutdown David A Case
- Re: [AMBER] Restarting PMEMD calculation after server shutdown Jason Swails
- Re: [AMBER] Problem in Amber12 and Amber12tools parallel installation in mac OS X 10.5 Prabu Manoharan
- Re: [AMBER] Problem in Amber12 and Amber12tools parallel installation in mac OS X 10.5 David A Case
- Re: [AMBER] AMBER on GPU: What is the maximum no. of nodes tested? Scott Le Grand
- Re: [AMBER] laptop GPU support Scott Le Grand
- [AMBER] Looking for parameters for a metal-organic compound Kat Russell
- Re: [AMBER] NPT equilibration error: ASSERTion 'e' failed in nonbond_list.F90 at line 849 Maria Minakova
- Re: [AMBER] FW: frcmod and lib files fro Cadmium Mahendra B Thapa
- [AMBER] Amber force field for PNIPAM Ganesh Kamath
- Re: [AMBER] Diverging sander.MPI results according to core allocation Jason Swails
Friday, 3 August 2012
- Re: [AMBER] Amber force field for PNIPAM Vishal Maingi
- [AMBER] Switch-off PBC in md-GPU Adam Jion
- Re: [AMBER] Switch-off PBC in md-GPU David A Case
- [AMBER] problem for MMPBSA.py in AmberTools12 zhenquan hu
- Re: [AMBER] problem for MMPBSA.py in AmberTools12 Bill Miller III
- [AMBER] TI run energy does not conserve Pin-Chih Su (Henry Su)
- [AMBER] to draw vector along the axis Sangita Kachhap
- Re: [AMBER] TI run energy does not conserve Brian Radak
- Re: [AMBER] Diverging sander.MPI results according to core allocation Bashford, Donald
- Re: [AMBER] Diverging sander.MPI results according to core allocation Jason Swails
- [AMBER] Reflective Boundary Conditions Adam Jion
Saturday, 4 August 2012
- [AMBER] non integer charge in antechamber generated mol2 file Raik Grünberg
- Re: [AMBER] non integer charge in antechamber generated mol2 file Raik Grünberg
- Re: [AMBER] Problems parameterizing water/ZN active site with MKT++ Ben Roberts
Sunday, 5 August 2012
- Re: [AMBER] Reflective Boundary Conditions case
- Re: [AMBER] Problems parameterizing water/ZN active site with MKT++ Fabrício Bracht
- Re: [AMBER] Reflective Boundary Conditions Dr. Vitaly V. G. Chaban
- [AMBER] angles and dihedrals for lone pairs Ivanov, Maxim
- Re: [AMBER] Problems parameterizing water/ZN active site with MKT++ Ben Roberts
- Re: [AMBER] problem for MMPBSA.py in AmberTools12 zhenquan hu
Monday, 6 August 2012
- [AMBER] TMD setup Manish Datt
- Re: [AMBER] TMD setup Simon Becker
- [AMBER] Extreme large scale movement of a residue Acoot Brett
- Re: [AMBER] angles and dihedrals for lone pairs case
- [AMBER] charge derivation for simulations in organic solvents Igor Pochorovski
- Re: [AMBER] charge derivation for simulations in organic solvents Dr. Vitaly V. G. Chaban
- Re: [AMBER] charge derivation for simulations in organic solvents Dr. Vitaly V. G. Chaban
- [AMBER] Amber12 parallel running issues Prabu Manoharan
- Re: [AMBER] Amber12 parallel running issues Miguel Ortiz Lombardia
- Re: [AMBER] TI run energy does not conserve Pin-Chih Su (Henry Su)
- [AMBER] Aspartate and Glutamate naming in PDB Zalikha Ibrahim
- Re: [AMBER] Aspartate and Glutamate naming in PDB Carlos Simmerling
- Re: [AMBER] non integer charge in antechamber generated mol2 file case
- Re: [AMBER] Aspartate and Glutamate naming in PDB Zalikha Ibrahim
Tuesday, 7 August 2012
- [AMBER] myristoyl lipid11/12 (DMPC) Vishal Maingi
- Re: [AMBER] Aspartate and Glutamate naming in PDB Carlos Simmerling
- [AMBER] lipid params and paper Gould, Ian R
- Re: [AMBER] lipid params and paper Albert
- [AMBER] MMPSA: PB Bomb in pb_aaradi(): ... Vlad Cojocaru
- Re: [AMBER] myristoyl lipid11/12 (DMPC) Vishal Maingi
- Re: [AMBER] MMPSA: PB Bomb in pb_aaradi(): ... Jason Swails
- Re: [AMBER] MMPSA: PB Bomb in pb_aaradi(): ... Vlad Cojocaru
- Re: [AMBER] TI run energy does not conserve Brian Radak
- Re: [AMBER] MMPSA: PB Bomb in pb_aaradi(): ... Jason Swails
- Re: [AMBER] MMPSA: PB Bomb in pb_aaradi(): ... Niel Henriksen
- Re: [AMBER] MMPSA: PB Bomb in pb_aaradi(): ... Vlad Cojocaru
- Re: [AMBER] MMPSA: PB Bomb in pb_aaradi(): ... Jason Swails
- Re: [AMBER] MMPSA: PB Bomb in pb_aaradi(): ... Vlad Cojocaru
- [AMBER] Looking for parameters Kat Russell
- [AMBER] MMPBSA, nonpolar solvation free energy inp=1 versus inp=2 Vlad Cojocaru
- [AMBER] AMBER 12 Documentation detail missing Aron Broom
- Re: [AMBER] MMPSA: PB Bomb in pb_aaradi(): ... Ray Luo, Ph.D.
- Re: [AMBER] MMPSA: PB Bomb in pb_aaradi(): ... Ray Luo, Ph.D.
- Re: [AMBER] MMPSA: PB Bomb in pb_aaradi(): ... Ray Luo, Ph.D.
- Re: [AMBER] angles and dihedrals for lone pairs Ivanov, Maxim
- Re: [AMBER] MMPBSA, nonpolar solvation free energy inp=1 versus inp=2 Ray Luo, Ph.D.
- Re: [AMBER] angles and dihedrals for lone pairs case
- [AMBER] Test message please ignore Ross Walker
- Re: [AMBER] MMPBSA, nonpolar solvation free energy inp=1 versus inp=2 Vlad Cojocaru
Wednesday, 8 August 2012
- [AMBER] Restraint problem Fernando Martín García
- Re: [AMBER] Restraint problem Jérôme Golebiowski
- Re: [AMBER] Restraint problem Fernando Martín García
- Re: [AMBER] Restraint problem Anselm Horn
- Re: [AMBER] Restraint problem Jason Swails
- Re: [AMBER] Restraint problem Fernando Martín García
- Re: [AMBER] Restraint problem case
- [AMBER] polarizable force field 旭东肖
- [AMBER] how to make a certain ionic concentration for the system? Kong, Ren
- Re: [AMBER] TI with softcore at lambda=0 or 1? Liu Denis
- [AMBER] question about calculation of PMF with WHAM Yan Li
- [AMBER] Starting and ending temperatures for REMD Sajeewa Pemasinghe
- Re: [AMBER] non integer charge in antechamber generated mol2 file Raik Grünberg
- Re: [AMBER] how to make a certain ionic concentration for the system? Brian Radak
- Re: [AMBER] how to make a certain ionic concentration for the system? Aron Broom
- Re: [AMBER] question about calculation of PMF with WHAM Brian Radak
- Re: [AMBER] TI run energy does not conserve Pin-Chih Su (Henry Su)
- Re: [AMBER] polarizable force field Yong Duan
- [AMBER] resp charge calculation jit mukherjee
- Re: [AMBER] polarizable force field 旭东肖
- Re: [AMBER] question about calculation of PMF with WHAM Yan Li
Thursday, 9 August 2012
- Re: [AMBER] TI with softcore at lambda=0 or 1? steinbrt.rci.rutgers.edu
- Re: [AMBER] TI with softcore at lambda=0 or 1? Liu Denis
- Re: [AMBER] TI run energy does not conserve Brian Radak
- Re: [AMBER] TI with softcore at lambda=0 or 1? steinbrt.rci.rutgers.edu
- Re: [AMBER] non integer charge in antechamber generated mol2 file FyD
- Re: [AMBER] resp charge calculation FyD
- Re: [AMBER] how to make a certain ionic concentration for the system? Kong, Ren
- Re: [AMBER] how to make a certain ionic concentration for the system? Kong, Ren
- Re: [AMBER] Looking for parameters FyD
- [AMBER] Have any one used the Nmode to calculate the entropy? Kong, Ren
- Re: [AMBER] Have any one used the Nmode to calculate the entropy? Jason Swails
- [AMBER] How to save Eigenvectors of modes using MMPBSA.py script? habi
- Re: [AMBER] Have any one used the Nmode to calculate the entropy? Matthew Tessier
- Re: [AMBER] question about calculation of PMF with WHAM Daniel Sindhikara
- [AMBER] How to recover box information from pdb with truncated octahedron solvent? Liu Denis
- [AMBER] Problem while using acdoctor command Sumra Wajid Abbasi 30-FBAS/MSBI/F09
Friday, 10 August 2012
- Re: [AMBER] TI run energy does not conserve psu4.uic.edu
- [AMBER] Errors during minimization (rfree: Error decoding variable 1 3) Zalikha Ibrahim
- Re: [AMBER] Errors during minimization (rfree: Error decoding variable 1 3) Terry
- Re: [AMBER] Restraint problem Fernando Martín García
- Re: [AMBER] non integer charge in antechamber generated mol2 file case
- Re: [AMBER] Errors during minimization (rfree: Error decoding variable 1 3) Jason Swails
- Re: [AMBER] Problems parameterizing water/ZN active site with MKT++ Fabrício Bracht
- Re: [AMBER] TI run energy does not conserve Brian Radak
- [AMBER] unique atom names Chris Chris
- [AMBER] specific atom restraint Thanh Binh NGUYEN
- Re: [AMBER] specific atom restraint Jason Swails
- Re: [AMBER] TI run energy does not conserve psu4.uic.edu
- Re: [AMBER] unique atom names case
- Re: [AMBER] specific atom restraint Thanh Binh NGUYEN
- Re: [AMBER] non integer charge in antechamber generated mol2 file Raik Grünberg
- Re: [AMBER] non integer charge in antechamber generated mol2 file Raik Grünberg
Saturday, 11 August 2012
- [AMBER] Installation of Amber11 Meena Singh
- Re: [AMBER] Installation of Amber11 case
- Re: [AMBER] TI with softcore at lambda=0 or 1? Liu Denis
Sunday, 12 August 2012
- Re: [AMBER] Problems parameterizing water/ZN active site with MKT++ Ben Roberts
- Re: [AMBER] TI with softcore at lambda=0 or 1? case
- Re: [AMBER] TI with softcore at lambda=0 or 1? Liu Denis
- Re: [AMBER] TI run energy does not conserve Brian Radak
Monday, 13 August 2012
- Re: [AMBER] Problems parameterizing water/ZN active site with MKT++ Ben Roberts
- [AMBER] Production md ariana karakutuk
- Re: [AMBER] Production md case
- [AMBER] Internal energy linear increase with temperature Binwu Zhao
- Re: [AMBER] Internal energy linear increase with temperature David A Case
- Re: [AMBER] non integer charge in antechamber generated mol2 file FyD
- [AMBER] General question George Tzotzos
- Re: [AMBER] General question Jason Swails
Tuesday, 14 August 2012
- Re: [AMBER] Production md ariana karakutuk
- Re: [AMBER] General question Gould, Ian R
- Re: [AMBER] General question George Tzotzos
- [AMBER] Query about how to run ambertools12 after installing it Yousef Elsyid
- Re: [AMBER] Production md David A Case
- Re: [AMBER] TI with softcore at lambda=0 or 1? David A Case
- Re: [AMBER] Problem while using acdoctor command David A Case
- Re: [AMBER] Query about how to run ambertools12 after installing it David A Case
- [AMBER] RMS fit Eliac Brown
- Re: [AMBER] RMS fit Daniel Roe
- Re: [AMBER] RMS fit Eliac Brown
- Re: [AMBER] RMS fit Jason Swails
- Re: [AMBER] RMS fit Daniel Roe
- Re: [AMBER] Problems parameterizing water/ZN active site with MKT++ Fabrício Bracht
- [AMBER] Problems when using cpptraj for reimaging when INPCRD file is one of the input frames Marek Maly
- Re: [AMBER] Problems parameterizing water/ZN active site with MKT++ Ben Roberts
- Re: [AMBER] Problems when using cpptraj for reimaging when INPCRD file is one of the input frames Daniel Roe
- [AMBER] which part of source code implementing GB/SA simulations? Xin Geng
- Re: [AMBER] TI with softcore at lambda=0 or 1? Liu Denis
- Re: [AMBER] which part of source code implementing GB/SA simulations? case
- [AMBER] which part of source code implementing GB/SA simulations? Xin Geng
- Re: [AMBER] which part of source code implementing GB/SA simulations? Xin Geng
- [AMBER] job in multiple GPUs Vijay Manickam Achari
Wednesday, 15 August 2012
- [AMBER] Fatal error (Could not read velocities) during heating Zalikha Ibrahim
- Re: [AMBER] Problems when using cpptraj for reimaging when INPCRD file is one of the input frames Marek Maly
- Re: [AMBER] Fatal error (Could not read velocities) during heating David A Case
- Re: [AMBER] Fatal error (Could not read velocities) during heating Jason Swails
- [AMBER] Temperature regulation in HREMD Brian Radak
- Re: [AMBER] Problems when using cpptraj for reimaging when INPCRD file is one of the input frames Daniel Roe
- Re: [AMBER] Problems when using cpptraj for reimaging when INPCRD file is one of the input frames Marek Maly
- [AMBER] PRMTOP TO PSF manikanthan bhavaraju
- Re: [AMBER] Temperature regulation in HREMD dani sd
- [AMBER] meaning of "tolerance" in REMD Sajeewa Pemasinghe
- Re: [AMBER] Problems when using cpptraj for reimaging when INPCRD file is one of the input frames Daniel Roe
- Re: [AMBER] Temperature regulation in HREMD Carlos Simmerling
- Re: [AMBER] Problems when using cpptraj for reimaging when INPCRD file is one of the input frames Daniel Roe
- Re: [AMBER] Temperature regulation in HREMD dani sd
- [AMBER] amber10 install Qian Wang
- Re: [AMBER] Problems when using cpptraj for reimaging when INPCRD file is one of the input frames Marek Maly
- Re: [AMBER] PRMTOP TO PSF case
- Re: [AMBER] amber10 install case
- [AMBER] how to predict time for MMPBSA decomp analysis vaibhav dixit
Thursday, 16 August 2012
- Re: [AMBER] Production md ariana karakutuk
- Re: [AMBER] Production md David A Case
- Re: [AMBER] amber10 install Qian Wang
- Re: [AMBER] amber10 install David A Case
- Re: [AMBER] amber10 install Qian Wang
- Re: [AMBER] how to predict time for MMPBSA decomp analysis Jason Swails
- [AMBER] MBAR calculation Liu Denis
- Re: [AMBER] MBAR calculation Brian Radak
- Re: [AMBER] how to predict time for MMPBSA decomp analysis vaibhav dixit
- [AMBER] Fwd: meaning of "tolerance" in REMD Sajeewa Pemasinghe
- Re: [AMBER] Fwd: meaning of "tolerance" in REMD Brian Radak
- [AMBER] Help with ncsu_abmd flooding mode Fabrício Bracht
- Re: [AMBER] Fwd: meaning of "tolerance" in REMD Sajeewa Pemasinghe
- Re: [AMBER] Fwd: meaning of "tolerance" in REMD Niel Henriksen
- Re: [AMBER] Fwd: meaning of "tolerance" in REMD Jason Swails
Friday, 17 August 2012
- [AMBER] Zn atom flying off moitrayee.mbu.iisc.ernet.in
- Re: [AMBER] Problems when using cpptraj for reimaging when INPCRD file is one of the input frames Daniel Roe
- Re: [AMBER] Problems when using cpptraj for reimaging when INPCRD file is one of the input frames Marek Maly
- [AMBER] nmode - calculation of vibrational frequencies Svetlana Oard
- [AMBER] Calculating Energy of an atom selection Aron Broom
- [AMBER] COM coordinates Vishal Maingi
Saturday, 18 August 2012
- [AMBER] where is the subroutine amflsh in Amber10? Xin Geng
- [AMBER] Flag for saving particular residues. HIMANSHU JOSHI
Sunday, 19 August 2012
- Re: [AMBER] where is the subroutine amflsh in Amber10? case
- Re: [AMBER] Flag for saving particular residues. case
- [AMBER] Error message in cpptraj when running at single node in supercomputer using mpirun Catein Catherine
- Re: [AMBER] FW: Re: How to Calculate SASA with Amber? E. Nihal Korkmaz
- Re: [AMBER] FW: Re: How to Calculate SASA with Amber? E. Nihal Korkmaz
- Re: [AMBER] FW: Re: How to Calculate SASA with Amber? Ross Walker
- Re: [AMBER] FW: Re: How to Calculate SASA with Amber? Jason Swails
- Re: [AMBER] Error message in cpptraj when running at single node in supercomputer using mpirun Jason Swails
- Re: [AMBER] FW: Re: How to Calculate SASA with Amber? Daniel Roe
- [AMBER] Accelerated Molecular Dynamics in Amber12 Soumya Lipsa Rath
- Re: [AMBER] Accelerated Molecular Dynamics in Amber12 Ross Walker
- Re: [AMBER] Error message in cpptraj when running at single node in supercomputer using mpirun Catein Catherine
Monday, 20 August 2012
- [AMBER] How to get the averaged structure of each cluster with cpptraj? Catein Catherine
- Re: [AMBER] Accelerated Molecular Dynamics in Amber12 Soumya Lipsa Rath
- Re: [AMBER] pbsa: how to increase the sampling volume (grid dimensions)? Jan-Philip Gehrcke
- Re: [AMBER] How to get the averaged structure of each cluster with cpptraj? Daniel Roe
- Re: [AMBER] Have any one used the Nmode to calculate the entropy? Matthew Tessier
- Re: [AMBER] Internal energy linear increase with temperature (David A Case) Binwu Zhao
- Re: [AMBER] Internal energy linear increase with temperature (David A Case) David A Case
- [AMBER] pmemd.cuda and nmropt Larry Olson
- Re: [AMBER] pmemd.cuda and nmropt Ross Walker
- [AMBER] transition metal system works on pmemd crashes on pmemd.cuda Patrick von Glehn
- Re: [AMBER] transition metal system works on pmemd crashes on pmemd.cuda Scott Le Grand
- Re: [AMBER] how to predict time for MMPBSA decomp analysis vaibhav dixit
- Re: [AMBER] how to predict time for MMPBSA decomp analysis Soumya Lipsa Rath
Tuesday, 21 August 2012
- Re: [AMBER] how to predict time for MMPBSA decomp analysis Jiri Sponer
- Re: [AMBER] COM coordinates Vishal Maingi
- [AMBER] AMBER alanine scan with chlorine Mannan
- Re: [AMBER] AMBER alanine scan with chlorine Bill Miller III
- [AMBER] Recommendations for Amber on AMD Bulldozer Jan-Philip Gehrcke
- Re: [AMBER] Recommendations for Amber on AMD Bulldozer Ross Walker
- Re: [AMBER] Recommendations for Amber on AMD Bulldozer Jan-Philip Gehrcke
- Re: [AMBER] COM coordinates Daniel Roe
- [AMBER] amber10 install (mpi) Qian Wang
- Re: [AMBER] amber10 install (mpi) Jason Swails
- [AMBER] area per lipid popc membrane Fabrício Bracht
- Re: [AMBER] amber10 install (mpi) Qian Wang
- Re: [AMBER] amber10 install (mpi) Jason Swails
- Re: [AMBER] amber10 install (mpi) Qian Wang
- Re: [AMBER] amber10 install (mpi) Jason Swails
- Re: [AMBER] amber10 install (mpi) case
- Re: [AMBER] nmode - calculation of vibrational frequencies case
- Re: [AMBER] MMPBSA.py gbsa unrecognized E. Nihal Korkmaz
- Re: [AMBER] MMPBSA.py gbsa unrecognized Jason Swails
- [AMBER] Is there any guide/tutorial/review to decide input format for MD based on system under consideration vaibhav dixit
- Re: [AMBER] COM coordinates Vishal Maingi
Wednesday, 22 August 2012
- [AMBER] How to derive dihedral angle force constants by MCPB JiYuan Liu
- [AMBER] Diffenent EPB in MMPBSA result with Liu Denis
- [AMBER] NPT at high pressure Francesco Pietra
- Re: [AMBER] NPT at high pressure Jason Swails
- Re: [AMBER] pbsa: how to increase the sampling volume (grid dimensions)? Ray Luo
- Re: [AMBER] transition metal system works on pmemd crashes on pmemd.cuda Patrick von Glehn
- Re: [AMBER] NPT at high pressure Francesco Pietra
- Re: [AMBER] amber10 install (mpi) Qian Wang
- Re: [AMBER] transition metal system works on pmemd crashes on pmemd.cuda Jason Swails
- [AMBER] Amber 12 cuda test suite: some tests 'hang' Jan-Philip Gehrcke
- Re: [AMBER] Amber 12 cuda test suite: some tests 'hang' Ross Walker
- Re: [AMBER] Amber 12 cuda test suite: some tests 'hang' Jan-Philip Gehrcke
- Re: [AMBER] Amber 12 cuda test suite: some tests 'hang' Scott Le Grand
- Re: [AMBER] Amber 12 cuda test suite: some tests 'hang' Jan-Philip Gehrcke
- Re: [AMBER] Amber 12 cuda test suite: some tests 'hang' Ross Walker
- Re: [AMBER] Diffenent EPB in MMPBSA result with Liu Denis
- Re: [AMBER] Diffenent EPB in MMPBSA result with Miguel Ortiz Lombardia
- Re: [AMBER] area per lipid popc membrane Benjamin D Madej
- Re: [AMBER] Amber 12 cuda test suite: some tests 'hang' Jan-Philip Gehrcke
- [AMBER] protein+DNA simulation najmul arfin
- [AMBER] Help about the igb Elaine Cheung
- Re: [AMBER] Amber 12 cuda test suite: some tests 'hang' Ross Walker
- Re: [AMBER] Amber 12 cuda test suite: some tests 'hang' Jan-Philip Gehrcke
- [AMBER] problem w/ radial results E. Nihal Korkmaz
- Re: [AMBER] problem w/ radial results Thomas Cheatham III
- Re: [AMBER] protein+DNA simulation Thomas Cheatham III
- Re: [AMBER] Help about the igb Carlos Simmerling
- Re: [AMBER] area per lipid popc membrane Fabrício Bracht
- Re: [AMBER] How to derive dihedral angle force constants by MCPB Ben Roberts
- Re: [AMBER] area per lipid popc membrane Benjamin D Madej
- Re: [AMBER] Help about the igb Elaine Cheung
- Re: [AMBER] area per lipid popc membrane jojartb.jgypk.u-szeged.hu
- Re: [AMBER] area per lipid popc membrane Albert
- [AMBER] loading of a mutant protein in XLEaP gargi borgohai
Thursday, 23 August 2012
- Re: [AMBER] area per lipid popc membrane Dickson, Callum
- [AMBER] More RMS fit George Tzotzos
- [AMBER] RECALL More RMS fit George Tzotzos
- Re: [AMBER] loading of a mutant protein in XLEaP Jason Swails
- [AMBER] ptraj: msd with diffusion command Bala subramanian
- [AMBER] amber 12 installation error Shuyi Cao
- [AMBER] failed to config serial amber 12 on IBM POWER7 Yubo Fan
- Re: [AMBER] protein+DNA simulation Dean Cuebas
- Re: [AMBER] nmode - calculation of vibrational frequencies Svetlana Oard
- Re: [AMBER] Diffenent EPB in MMPBSA result with Qin Cai
- [AMBER] Different Properties Value with Tesla vs GeForce GPUs Ismail, Mohd F.
- Re: [AMBER] amber 12 installation error Jason Swails
- [AMBER] AMBER Workshop Announcement - Oct 8th to 12th - Lausanne Switzerland Ross Walker
- Re: [AMBER] AMBER Workshop Announcement - Oct 8th to 12th - Lausanne Switzerland Albert
- Re: [AMBER] AMBER Workshop Announcement - Oct 8th to 12th - Lausanne Switzerland Ross Walker
- Re: [AMBER] ptraj: msd with diffusion command Daniel Roe
- [AMBER] parallel installation problem: Amber11+AmberTools1.4 on a linux cluster Alfred Zheng
- Re: [AMBER] parallel installation problem: Amber11+AmberTools1.4 on a linux cluster Jason Swails
- [AMBER] about ions Carlos Romero
- [AMBER] failed to config serial amber 12 on IBM POWER7 Yubo Fan
Friday, 24 August 2012
- Re: [AMBER] AMBER Workshop Announcement - Oct 8th to 12th - Lausanne Switzerland Albert
- Re: [AMBER] about ions David A Case
- Re: [AMBER] failed to config serial amber 12 on IBM POWER7 David A Case
- [AMBER] cpptraj surf George Tzotzos
- Re: [AMBER] Amber 12 cuda test suite: some tests 'hang' Robert Crovella
- Re: [AMBER] cpptraj surf Daniel Roe
- Re: [AMBER] cpptraj surf George Tzotzos
- [AMBER] parallel constraints SMD e g
- Re: [AMBER] cpptraj surf Jason Swails
- Re: [AMBER] parallel constraints SMD Jason Swails
- Re: [AMBER] cpptraj surf George Tzotzos
- Re: [AMBER] cpptraj surf Daniel Roe
- Re: [AMBER] cpptraj surf George Tzotzos
- Re: [AMBER] cpptraj surf Jason Swails
- Re: [AMBER] parallel constraints SMD e g
- Re: [AMBER] about ions Carlos Romero
- Re: [AMBER] about ions Jason Swails
Saturday, 25 August 2012
- Re: [AMBER] Help about the igb Carlos Simmerling
- [AMBER] Can electrostatic potential of GBSA be visualized? Liu Denis
- Re: [AMBER] ptraj: msd with diffusion command Dmitry Mukha
Sunday, 26 August 2012
- Re: [AMBER] about ions Carlos Romero
- [AMBER] parallel run error najmul arfin
Monday, 27 August 2012
- [AMBER] CPPTRAJ: Is it a program that requires a large memory? Catein Catherine
- [AMBER] Decomposing the free energy contributions to the binding free energy Deák Robert
- [AMBER] GDP and MG parameters Vlad Cojocaru
- [AMBER] Can we use Ambertools analysis MD from GROMACS Acoot Brett
- Re: [AMBER] parallel run error Jason Swails
- Re: [AMBER] CPPTRAJ: Is it a program that requires a large memory? Jason Swails
- Re: [AMBER] Can we use Ambertools analysis MD from GROMACS Jason Swails
- Re: [AMBER] Can we use Ambertools analysis MD from GROMACS Pawel
- [AMBER] Help with ncsu_abmd flooding mode Fabrício Bracht
- Re: [AMBER] Help about the igb Elaine Cheung
- Re: [AMBER] Help with ncsu_abmd flooding mode Brian Radak
- Re: [AMBER] GDP and MG parameters George M Giambasu
- Re: [AMBER] Decomposing the free energy contributions to the binding free energy Liu Denis
- Re: [AMBER] Help with ncsu_abmd flooding mode Fabrício Bracht
- Re: [AMBER] Help with ncsu_abmd flooding mode Jason Swails
- Re: [AMBER] Decomposing the free energy contributions to the binding free energy Deák Robert
- Re: [AMBER] Help with ncsu_abmd flooding mode M. L. Dodson
- Re: [AMBER] Decomposing the free energy contributions to the binding free energy Liu Denis
- Re: [AMBER] CPPTRAJ: Is it a program that requires a large memory? Daniel Roe
- [AMBER] Particles diffuse very far away from each other ariana karakutuk
- Re: [AMBER] Particles diffuse very far away from each other Jason Swails
Tuesday, 28 August 2012
- Re: [AMBER] Decomposing the free energy contributions to the binding free energy Deák Robert
- Re: [AMBER] GDP and MG parameters FyD
- Re: [AMBER] GDP and MG parameters Vlad Cojocaru
- [AMBER] help about TMD 燕燕朱
- Re: [AMBER] help about TMD David A Case
- Re: [AMBER] Decomposing the free energy contributions to the binding free energy Jason Swails
- [AMBER] How can I get a average structure? Sanjib Paul
- Re: [AMBER] How can I get a average structure? Jason Swails
- [AMBER] Dummy atom and PMEMD Ali M. Naserian-Nik
- [AMBER] Can we use autoimage of cpptraj in AMBER 12? Catein Catherine
- Re: [AMBER] Can we use autoimage of cpptraj in AMBER 12? Jason Swails
- Re: [AMBER] How can I get a average structure? Sanjib Paul
- Re: [AMBER] How can I get a average structure? Daniel Roe
- Re: [AMBER] GDP and MG parameters FyD
- Re: [AMBER] How can I get a average structure? Sanjib Paul
- [AMBER] Problem regarding imin = 5 Sanjib Paul
- Re: [AMBER] Problem regarding imin = 5 Carlos Simmerling
- Re: [AMBER] Problem regarding imin = 5 Sanjib Paul
- Re: [AMBER] Problem regarding imin = 5 Sanjib Paul
- Re: [AMBER] GDP and MG parameters Vlad Cojocaru
- [AMBER] MPI version of Amber on CPU provide different results in each run Mohammad Ashraf Bhuiyan
- [AMBER] "QMMM of protein-ligand complex: Unable to achieve self consistency" and "bond stretch too far" psu4.uic.edu
- Re: [AMBER] Dummy atom and PMEMD case
- Re: [AMBER] MPI version of Amber on CPU provide different results in each run Liu Denis
- [AMBER] Adding water molecules directly into files Adam Jion
- Re: [AMBER] Adding water molecules directly into files Liu Denis
- Re: [AMBER] Adding water molecules directly into files Jason Swails
- [AMBER] How to combine RMSF profiles? Catein Catherine
- Re: [AMBER] Dummy atom and PMEMD Ali M. Naserian-Nik
Wednesday, 29 August 2012
- Re: [AMBER] Adding water molecules directly into files Marc van der Kamp
- [AMBER] mpi4py import error mesage is improvable Jan-Philip Gehrcke
- [AMBER] Amber 12: CalcError in mmpbsa_py_energy and sander Jan-Philip Gehrcke
- [AMBER] problem to perform nmode analysis Sanjib Paul
- Re: [AMBER] problem to perform nmode analysis Sanjib Paul
- Re: [AMBER] Amber 12: CalcError in mmpbsa_py_energy and sander Jason Swails
- Re: [AMBER] mpi4py import error mesage is improvable Jason Swails
- [AMBER] CPPTRAJ hbond command Samuel Genheden
- Re: [AMBER] How to combine RMSF profiles? Jason Swails
- Re: [AMBER] How to combine RMSF profiles? Carlos Simmerling
- Re: [AMBER] problem to perform nmode analysis David A Case
- Re: [AMBER] problem to perform nmode analysis Jason Swails
- Re: [AMBER] problem to perform nmode analysis Sanjib Paul
- Re: [AMBER] CPPTRAJ hbond command Daniel Roe
- [AMBER] group specification for different force constants for different groups Sajeewa Pemasinghe
- Re: [AMBER] group specification for different force constants for different groups Jason Swails
- [AMBER] keeping parts of a protein virtually frozen in MD with pmemd Sajeewa Pemasinghe
- [AMBER] Amber12 Configuring NetCDF or fftw3 or MTK++ hang Yu Chen
- Re: [AMBER] Amber12 Configuring NetCDF or fftw3 or MTK++ hang Jason Swails
- Re: [AMBER] Amber12 Configuring NetCDF or fftw3 or MTK++ hang Ben Roberts
- Re: [AMBER] How to combine RMSF profiles? Catein Catherine
- Re: [AMBER] How to combine RMSF profiles? Jason Swails
- [AMBER] Installation problem of AmberTools of AMBER11 Sanjib Paul
Thursday, 30 August 2012
- Re: [AMBER] Installation problem of AmberTools of AMBER11 David A Case
- Re: [AMBER] Installation problem of AmberTools of AMBER11 Sanjib Paul
- Re: [AMBER] Installation problem of AmberTools of AMBER11 Jason Swails
- Re: [AMBER] Amber12 Configuring NetCDF or fftw3 or MTK++ hang Yu Chen
- Re: [AMBER] Amber12 Configuring NetCDF or fftw3 or MTK++ hang Jason Swails
- [AMBER] Bacteriochlorophyll parameters from Ceccarelli et al.? Marc van der Kamp
- Re: [AMBER] Installation problem of AmberTools of AMBER11 Sanjib Paul
- Re: [AMBER] Dummy atom and PMEMD David A Case
- Re: [AMBER] Installation problem of AmberTools of AMBER11 Jason Swails
- Re: [AMBER] Dummy atom and PMEMD Ali M. Naserian-Nik
- Re: [AMBER] Dummy atom and PMEMD Jason Swails
- [AMBER] RESP charge derivation shomesankar bhunia
- Re: [AMBER] RESP charge derivation Jason Swails
- Re: [AMBER] Installation problem of AmberTools of AMBER11 Sanjib Paul
- Re: [AMBER] RESP charge derivation shomesankar bhunia
- Re: [AMBER] Dummy atom and PMEMD Ali M. Naserian-Nik
- Re: [AMBER] RESP charge derivation Jason Swails
- Re: [AMBER] Installation problem of AmberTools of AMBER11 Jason Swails
- Re: [AMBER] Dummy atom and PMEMD Jason Swails
- [AMBER] Segmentation Fault in Tleap Deepak Ojha
- Re: [AMBER] Segmentation Fault in Tleap Jason Swails
- [AMBER] ions concenration Carlos Romero
- Re: [AMBER] RESP charge derivation shomesankar bhunia
- Re: [AMBER] Installation problem of AmberTools of AMBER11 Sanjib Paul
- Re: [AMBER] RESP charge derivation shomesankar bhunia
- Re: [AMBER] RESP charge derivation FyD
- Re: [AMBER] RESP charge derivation shomesankar bhunia
- [AMBER] How to choose a particular region to minimization? Thanh Binh NGUYEN
Friday, 31 August 2012
- Re: [AMBER] Dummy atom and PMEMD Ali M. Naserian-Nik
- Re: [AMBER] How to choose a particular region to minimization? Marc van der Kamp
- Re: [AMBER] How to choose a particular region to minimization? Thanh Binh NGUYEN
- Re: [AMBER] Dummy atom and PMEMD David A Case
- Re: [AMBER] Installation problem of AmberTools of AMBER11 David A Case
- Re: [AMBER] Amber 12: CalcError in mmpbsa_py_energy and sander Jan-Philip Gehrcke
- Re: [AMBER] Amber 12: CalcError in mmpbsa_py_energy and sander Jason Swails
- [AMBER] newbie question: simulating miRNA Michiel de Hoon
- Re: [AMBER] How to choose a particular region to minimization? Jason Swails
- Re: [AMBER] ions concenration Daniel Sindhikara
- [AMBER] ERROR: max pairlist cutoff must be less than unit cell max sphere radius! Gabriel Jara
- Re: [AMBER] ERROR: max pairlist cutoff must be less than unit cell max sphere radius! Brian Radak
- Re: [AMBER] Amber 12: CalcError in mmpbsa_py_energy and sander Jan-Philip Gehrcke
- Re: [AMBER] ions concenration Marek Maly
- Re: [AMBER] ions concenration Carlos Romero
- Re: [AMBER] Amber 12: CalcError in mmpbsa_py_energy and sander Jason Swails
- Re: [AMBER] newbie question: simulating miRNA Niel Henriksen
- Re: [AMBER] Amber 12: CalcError in mmpbsa_py_energy and sander Jan-Philip Gehrcke
- Re: [AMBER] Amber 12: CalcError in mmpbsa_py_energy and sander Ray Luo, Ph.D.
- Re: [AMBER] ions concenration Carlos Romero
- Re: [AMBER] ptraj: msd with diffusion command Bala subramanian
- Re: [AMBER] Diffenent EPB in MMPBSA result with Qin Cai
- Re: [AMBER] newbie question: simulating miRNA David A Case
- Re: [AMBER] newbie question: simulating miRNA Niel Henriksen
- Re: [AMBER] ERROR: max pairlist cutoff must be less than unit cell max sphere radius! Gabriel Jara
- Re: [AMBER] ERROR: max pairlist cutoff must be less than unit cell max sphere radius! case

Last message date: Fri Aug 31 2012 - 16:00:03 PDT
Archived on: Sun Nov 17 2024 - 05:54:36 PST

Amber Archive Aug 2012 by date