Amber Archive Aug 2012 by thread
475 messages
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Starting
Tue Jul 31 2012 - 20:30:03 PDT,
Ending
Fri Aug 31 2012 - 16:00:03 PDT
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[AMBER] cpptraj: autoimage + anchor works very well.
Catein Catherine
(Tue Jul 31 2012 - 20:23:37 PDT)
[AMBER] how to include derived charges in AMBER
Sanjib Paul
(Tue Jul 31 2012 - 23:52:02 PDT)
[AMBER] laptop GPU support
Thomas Evangelidis
(Wed Aug 01 2012 - 03:08:52 PDT)
[AMBER] AMBER on GPU: What is the maximum no. of nodes tested?
Catein Catherine
(Wed Aug 01 2012 - 03:40:19 PDT)
Re: [AMBER] AMBER on GPU: What is the maximum no. of nodes tested?
Scott Le Grand
(Thu Aug 02 2012 - 08:00:08 PDT)
Re: [AMBER] laptop GPU support
Jason Swails
(Wed Aug 01 2012 - 05:29:10 PDT)
Re: [AMBER] laptop GPU support
Benjamin D Madej
(Wed Aug 01 2012 - 11:14:05 PDT)
Re: [AMBER] laptop GPU support
Scott Le Grand
(Thu Aug 02 2012 - 08:04:43 PDT)
[AMBER] Problem in Amber12 and Amber12tools parallel installation in mac OS X 10.5
Prabu Manoharan
(Wed Aug 01 2012 - 06:01:02 PDT)
Re: [AMBER] Problem in Amber12 and Amber12tools parallel installation in mac OS X 10.5
Jason Swails
(Wed Aug 01 2012 - 06:10:20 PDT)
Re: [AMBER] Problem in Amber12 and Amber12tools parallel installation in mac OS X 10.5
David A Case
(Wed Aug 01 2012 - 07:08:29 PDT)
Re: [AMBER] Problem in Amber12 and Amber12tools parallel installation in mac OS X 10.5
Prabu Manoharan
(Thu Aug 02 2012 - 05:48:32 PDT)
Re: [AMBER] Problem in Amber12 and Amber12tools parallel installation in mac OS X 10.5
David A Case
(Thu Aug 02 2012 - 07:41:59 PDT)
[AMBER] receptor nmode calculation using amber12 mmpbsa.pl
manikanthan bhavaraju
(Wed Aug 01 2012 - 10:36:55 PDT)
Re: [AMBER] receptor nmode calculation using amber12 mmpbsa.pl
Jason Swails
(Wed Aug 01 2012 - 10:52:32 PDT)
[AMBER] non polar solvation energy
kirtana S
(Wed Aug 01 2012 - 12:26:03 PDT)
[AMBER] large difference between MMGBSA and MMPBSA free energy
Kong, Ren
(Wed Aug 01 2012 - 12:26:02 PDT)
Re: [AMBER] large difference between MMGBSA and MMPBSA free energy
Ray Luo, Ph.D.
(Wed Aug 01 2012 - 12:38:44 PDT)
Re: [AMBER] large difference between MMGBSA and MMPBSA free energy
Kong, Ren
(Wed Aug 01 2012 - 13:45:36 PDT)
Re: [AMBER] large difference between MMGBSA and MMPBSA free energy
Ray Luo, Ph.D.
(Wed Aug 01 2012 - 14:45:45 PDT)
[AMBER] frcmod and lib files fro Cadmium
Mahendra B Thapa
(Wed Aug 01 2012 - 13:08:54 PDT)
Re: [AMBER] frcmod and lib files fro Cadmium
Kong, Ren
(Wed Aug 01 2012 - 13:39:20 PDT)
Re: [AMBER] FW: problem in converting rst-file to pdb using cpptraj
Mahendra B Thapa
(Wed Aug 01 2012 - 14:18:58 PDT)
[AMBER] make test query
vaibhav dixit
(Thu Aug 02 2012 - 02:40:39 PDT)
Re: [AMBER] Making a complex
Saaz Sakrikar
(Thu Aug 02 2012 - 04:00:49 PDT)
Re: [AMBER] Making a complex
David A Case
(Thu Aug 02 2012 - 05:00:52 PDT)
[AMBER] Restarting PMEMD calculation after server shutdown
Saaz Sakrikar
(Thu Aug 02 2012 - 04:07:15 PDT)
Re: [AMBER] Restarting PMEMD calculation after server shutdown
David A Case
(Thu Aug 02 2012 - 05:05:01 PDT)
Re: [AMBER] Restarting PMEMD calculation after server shutdown
Jason Swails
(Thu Aug 02 2012 - 05:17:38 PDT)
[AMBER] Looking for parameters for a metal-organic compound
Kat Russell
(Thu Aug 02 2012 - 11:10:08 PDT)
Re: [AMBER] NPT equilibration error: ASSERTion 'e' failed in nonbond_list.F90 at line 849
Maria Minakova
(Thu Aug 02 2012 - 12:11:17 PDT)
Re: [AMBER] FW: frcmod and lib files fro Cadmium
Mahendra B Thapa
(Thu Aug 02 2012 - 14:07:11 PDT)
[AMBER] Amber force field for PNIPAM
Ganesh Kamath
(Thu Aug 02 2012 - 16:36:10 PDT)
Re: [AMBER] Amber force field for PNIPAM
Vishal Maingi
(Fri Aug 03 2012 - 03:25:18 PDT)
Re: [AMBER] Diverging sander.MPI results according to core allocation
Jason Swails
(Thu Aug 02 2012 - 20:41:41 PDT)
Re: [AMBER] Diverging sander.MPI results according to core allocation
Bashford, Donald
(Fri Aug 03 2012 - 12:12:10 PDT)
Re: [AMBER] Diverging sander.MPI results according to core allocation
Jason Swails
(Fri Aug 03 2012 - 13:22:55 PDT)
[AMBER] Switch-off PBC in md-GPU
Adam Jion
(Fri Aug 03 2012 - 03:42:18 PDT)
Re: [AMBER] Switch-off PBC in md-GPU
David A Case
(Fri Aug 03 2012 - 05:17:07 PDT)
[AMBER] problem for MMPBSA.py in AmberTools12
zhenquan hu
(Fri Aug 03 2012 - 06:49:15 PDT)
Re: [AMBER] problem for MMPBSA.py in AmberTools12
Bill Miller III
(Fri Aug 03 2012 - 07:17:10 PDT)
Re: [AMBER] problem for MMPBSA.py in AmberTools12
zhenquan hu
(Sun Aug 05 2012 - 23:48:40 PDT)
[AMBER] TI run energy does not conserve
Pin-Chih Su (Henry Su)
(Fri Aug 03 2012 - 10:44:03 PDT)
Re: [AMBER] TI run energy does not conserve
Brian Radak
(Fri Aug 03 2012 - 11:44:40 PDT)
Re: [AMBER] TI run energy does not conserve
Pin-Chih Su (Henry Su)
(Mon Aug 06 2012 - 15:51:54 PDT)
Re: [AMBER] TI run energy does not conserve
Brian Radak
(Tue Aug 07 2012 - 07:09:53 PDT)
Re: [AMBER] TI run energy does not conserve
Pin-Chih Su (Henry Su)
(Wed Aug 08 2012 - 15:02:55 PDT)
Re: [AMBER] TI run energy does not conserve
Brian Radak
(Thu Aug 09 2012 - 07:30:48 PDT)
Re: [AMBER] TI run energy does not conserve
psu4.uic.edu
(Fri Aug 10 2012 - 00:16:10 PDT)
Re: [AMBER] TI run energy does not conserve
Brian Radak
(Fri Aug 10 2012 - 06:20:51 PDT)
Re: [AMBER] TI run energy does not conserve
psu4.uic.edu
(Fri Aug 10 2012 - 13:41:22 PDT)
Re: [AMBER] TI run energy does not conserve
Brian Radak
(Sun Aug 12 2012 - 12:14:34 PDT)
[AMBER] to draw vector along the axis
Sangita Kachhap
(Fri Aug 03 2012 - 10:54:53 PDT)
[AMBER] Reflective Boundary Conditions
Adam Jion
(Fri Aug 03 2012 - 21:17:50 PDT)
Re: [AMBER] Reflective Boundary Conditions
case
(Sun Aug 05 2012 - 07:13:30 PDT)
Re: [AMBER] Reflective Boundary Conditions
Dr. Vitaly V. G. Chaban
(Sun Aug 05 2012 - 13:16:27 PDT)
[AMBER] Extreme large scale movement of a residue
Acoot Brett
(Mon Aug 06 2012 - 03:38:42 PDT)
[AMBER] non integer charge in antechamber generated mol2 file
Raik Grünberg
(Sat Aug 04 2012 - 17:32:59 PDT)
Re: [AMBER] non integer charge in antechamber generated mol2 file
Raik Grünberg
(Sat Aug 04 2012 - 19:38:18 PDT)
Re: [AMBER] non integer charge in antechamber generated mol2 file
case
(Mon Aug 06 2012 - 18:28:13 PDT)
Re: [AMBER] non integer charge in antechamber generated mol2 file
Raik Grünberg
(Wed Aug 08 2012 - 10:41:14 PDT)
Re: [AMBER] non integer charge in antechamber generated mol2 file
case
(Fri Aug 10 2012 - 05:35:41 PDT)
Re: [AMBER] non integer charge in antechamber generated mol2 file
Raik Grünberg
(Fri Aug 10 2012 - 20:28:42 PDT)
Re: [AMBER] non integer charge in antechamber generated mol2 file
FyD
(Thu Aug 09 2012 - 08:53:54 PDT)
Re: [AMBER] non integer charge in antechamber generated mol2 file
Raik Grünberg
(Fri Aug 10 2012 - 20:43:02 PDT)
Re: [AMBER] non integer charge in antechamber generated mol2 file
FyD
(Mon Aug 13 2012 - 09:35:31 PDT)
Re: [AMBER] Problems parameterizing water/ZN active site with MKT++
Ben Roberts
(Sat Aug 04 2012 - 22:19:53 PDT)
Re: [AMBER] Problems parameterizing water/ZN active site with MKT++
Fabrício Bracht
(Sun Aug 05 2012 - 07:39:03 PDT)
Re: [AMBER] Problems parameterizing water/ZN active site with MKT++
Ben Roberts
(Sun Aug 05 2012 - 17:43:37 PDT)
Re: [AMBER] Problems parameterizing water/ZN active site with MKT++
Fabrício Bracht
(Fri Aug 10 2012 - 05:47:02 PDT)
Re: [AMBER] Problems parameterizing water/ZN active site with MKT++
Ben Roberts
(Sun Aug 12 2012 - 02:48:08 PDT)
Re: [AMBER] Problems parameterizing water/ZN active site with MKT++
Ben Roberts
(Mon Aug 13 2012 - 01:19:10 PDT)
Re: [AMBER] Problems parameterizing water/ZN active site with MKT++
Fabrício Bracht
(Tue Aug 14 2012 - 10:55:43 PDT)
Re: [AMBER] Problems parameterizing water/ZN active site with MKT++
Ben Roberts
(Tue Aug 14 2012 - 14:27:23 PDT)
[AMBER] angles and dihedrals for lone pairs
Ivanov, Maxim
(Sun Aug 05 2012 - 16:39:47 PDT)
Re: [AMBER] angles and dihedrals for lone pairs
case
(Mon Aug 06 2012 - 06:06:17 PDT)
Re: [AMBER] angles and dihedrals for lone pairs
Ivanov, Maxim
(Tue Aug 07 2012 - 15:19:48 PDT)
Re: [AMBER] angles and dihedrals for lone pairs
case
(Tue Aug 07 2012 - 18:52:12 PDT)
[AMBER] TMD setup
Manish Datt
(Mon Aug 06 2012 - 01:46:14 PDT)
Re: [AMBER] TMD setup
Simon Becker
(Mon Aug 06 2012 - 02:15:29 PDT)
[AMBER] charge derivation for simulations in organic solvents
Igor Pochorovski
(Mon Aug 06 2012 - 07:53:31 PDT)
Re: [AMBER] charge derivation for simulations in organic solvents
Dr. Vitaly V. G. Chaban
(Mon Aug 06 2012 - 07:58:22 PDT)
Re: [AMBER] charge derivation for simulations in organic solvents
Dr. Vitaly V. G. Chaban
(Mon Aug 06 2012 - 08:18:06 PDT)
[AMBER] Amber12 parallel running issues
Prabu Manoharan
(Mon Aug 06 2012 - 10:00:50 PDT)
Re: [AMBER] Amber12 parallel running issues
Miguel Ortiz Lombardia
(Mon Aug 06 2012 - 11:50:37 PDT)
[AMBER] Aspartate and Glutamate naming in PDB
Zalikha Ibrahim
(Mon Aug 06 2012 - 18:21:05 PDT)
Re: [AMBER] Aspartate and Glutamate naming in PDB
Carlos Simmerling
(Mon Aug 06 2012 - 18:23:41 PDT)
Re: [AMBER] Aspartate and Glutamate naming in PDB
Zalikha Ibrahim
(Mon Aug 06 2012 - 18:39:29 PDT)
Re: [AMBER] Aspartate and Glutamate naming in PDB
Carlos Simmerling
(Tue Aug 07 2012 - 04:43:27 PDT)
[AMBER] MMPBSA, nonpolar solvation free energy inp=1 versus inp=2
Vlad Cojocaru
(Tue Aug 07 2012 - 10:04:50 PDT)
Re: [AMBER] MMPBSA, nonpolar solvation free energy inp=1 versus inp=2
Ray Luo, Ph.D.
(Tue Aug 07 2012 - 15:22:58 PDT)
Re: [AMBER] MMPBSA, nonpolar solvation free energy inp=1 versus inp=2
Vlad Cojocaru
(Tue Aug 07 2012 - 22:45:05 PDT)
[AMBER] myristoyl lipid11/12 (DMPC)
Vishal Maingi
(Tue Aug 07 2012 - 01:48:36 PDT)
Re: [AMBER] myristoyl lipid11/12 (DMPC)
Vishal Maingi
(Tue Aug 07 2012 - 06:15:59 PDT)
[AMBER] lipid params and paper
Gould, Ian R
(Tue Aug 07 2012 - 05:08:54 PDT)
Re: [AMBER] lipid params and paper
Albert
(Tue Aug 07 2012 - 05:11:51 PDT)
[AMBER] MMPSA: PB Bomb in pb_aaradi(): ...
Vlad Cojocaru
(Tue Aug 07 2012 - 06:03:12 PDT)
Re: [AMBER] MMPSA: PB Bomb in pb_aaradi(): ...
Jason Swails
(Tue Aug 07 2012 - 06:34:54 PDT)
Re: [AMBER] MMPSA: PB Bomb in pb_aaradi(): ...
Vlad Cojocaru
(Tue Aug 07 2012 - 06:53:57 PDT)
Re: [AMBER] MMPSA: PB Bomb in pb_aaradi(): ...
Jason Swails
(Tue Aug 07 2012 - 07:21:39 PDT)
Re: [AMBER] MMPSA: PB Bomb in pb_aaradi(): ...
Niel Henriksen
(Tue Aug 07 2012 - 07:30:07 PDT)
Re: [AMBER] MMPSA: PB Bomb in pb_aaradi(): ...
Ray Luo, Ph.D.
(Tue Aug 07 2012 - 15:16:18 PDT)
Re: [AMBER] MMPSA: PB Bomb in pb_aaradi(): ...
Vlad Cojocaru
(Tue Aug 07 2012 - 07:32:57 PDT)
Re: [AMBER] MMPSA: PB Bomb in pb_aaradi(): ...
Jason Swails
(Tue Aug 07 2012 - 07:49:29 PDT)
Re: [AMBER] MMPSA: PB Bomb in pb_aaradi(): ...
Vlad Cojocaru
(Tue Aug 07 2012 - 07:58:25 PDT)
Re: [AMBER] MMPSA: PB Bomb in pb_aaradi(): ...
Ray Luo, Ph.D.
(Tue Aug 07 2012 - 15:17:15 PDT)
Re: [AMBER] MMPSA: PB Bomb in pb_aaradi(): ...
Ray Luo, Ph.D.
(Tue Aug 07 2012 - 15:15:38 PDT)
[AMBER] Looking for parameters
Kat Russell
(Tue Aug 07 2012 - 08:22:51 PDT)
Re: [AMBER] Looking for parameters
FyD
(Thu Aug 09 2012 - 09:54:38 PDT)
[AMBER] AMBER 12 Documentation detail missing
Aron Broom
(Tue Aug 07 2012 - 11:42:21 PDT)
[AMBER] Test message please ignore
Ross Walker
(Tue Aug 07 2012 - 22:21:36 PDT)
[AMBER] Restraint problem
Fernando Martín García
(Wed Aug 08 2012 - 02:53:15 PDT)
Re: [AMBER] Restraint problem
Jérôme Golebiowski
(Wed Aug 08 2012 - 03:13:51 PDT)
Re: [AMBER] Restraint problem
Fernando Martín García
(Wed Aug 08 2012 - 03:35:03 PDT)
Re: [AMBER] Restraint problem
Anselm Horn
(Wed Aug 08 2012 - 04:27:22 PDT)
Re: [AMBER] Restraint problem
Jason Swails
(Wed Aug 08 2012 - 05:09:53 PDT)
Re: [AMBER] Restraint problem
Fernando Martín García
(Wed Aug 08 2012 - 05:27:38 PDT)
Re: [AMBER] Restraint problem
case
(Wed Aug 08 2012 - 06:30:05 PDT)
Re: [AMBER] Restraint problem
Fernando Martín García
(Fri Aug 10 2012 - 02:59:43 PDT)
[AMBER] polarizable force field
旭东 肖
(Wed Aug 08 2012 - 06:46:13 PDT)
Re: [AMBER] polarizable force field
Yong Duan
(Wed Aug 08 2012 - 15:19:55 PDT)
Re: [AMBER] polarizable force field
旭东 肖
(Wed Aug 08 2012 - 18:18:18 PDT)
[AMBER] how to make a certain ionic concentration for the system?
Kong, Ren
(Wed Aug 08 2012 - 09:29:50 PDT)
Re: [AMBER] how to make a certain ionic concentration for the system?
Brian Radak
(Wed Aug 08 2012 - 12:26:09 PDT)
Re: [AMBER] how to make a certain ionic concentration for the system?
Kong, Ren
(Thu Aug 09 2012 - 09:45:28 PDT)
Re: [AMBER] how to make a certain ionic concentration for the system?
Aron Broom
(Wed Aug 08 2012 - 12:27:48 PDT)
Re: [AMBER] how to make a certain ionic concentration for the system?
Kong, Ren
(Thu Aug 09 2012 - 09:46:19 PDT)
Re: [AMBER] TI with softcore at lambda=0 or 1?
Liu Denis
(Wed Aug 08 2012 - 10:01:14 PDT)
Re: [AMBER] TI with softcore at lambda=0 or 1?
steinbrt.rci.rutgers.edu
(Thu Aug 09 2012 - 01:05:12 PDT)
Re: [AMBER] TI with softcore at lambda=0 or 1?
Liu Denis
(Thu Aug 09 2012 - 06:37:15 PDT)
Re: [AMBER] TI with softcore at lambda=0 or 1?
steinbrt.rci.rutgers.edu
(Thu Aug 09 2012 - 08:08:40 PDT)
Re: [AMBER] TI with softcore at lambda=0 or 1?
Liu Denis
(Sat Aug 11 2012 - 09:37:36 PDT)
Re: [AMBER] TI with softcore at lambda=0 or 1?
case
(Sun Aug 12 2012 - 05:55:20 PDT)
Re: [AMBER] TI with softcore at lambda=0 or 1?
Liu Denis
(Sun Aug 12 2012 - 08:01:33 PDT)
Re: [AMBER] TI with softcore at lambda=0 or 1?
David A Case
(Tue Aug 14 2012 - 05:22:53 PDT)
Re: [AMBER] TI with softcore at lambda=0 or 1?
Liu Denis
(Tue Aug 14 2012 - 18:29:16 PDT)
[AMBER] question about calculation of PMF with WHAM
Yan Li
(Wed Aug 08 2012 - 10:07:37 PDT)
Re: [AMBER] question about calculation of PMF with WHAM
Brian Radak
(Wed Aug 08 2012 - 13:11:19 PDT)
Re: [AMBER] question about calculation of PMF with WHAM
Yan Li
(Wed Aug 08 2012 - 18:43:02 PDT)
Re: [AMBER] question about calculation of PMF with WHAM
Daniel Sindhikara
(Thu Aug 09 2012 - 18:40:00 PDT)
[AMBER] Starting and ending temperatures for REMD
Sajeewa Pemasinghe
(Wed Aug 08 2012 - 10:26:56 PDT)
[AMBER] resp charge calculation
jit mukherjee
(Wed Aug 08 2012 - 17:44:13 PDT)
Re: [AMBER] resp charge calculation
FyD
(Thu Aug 09 2012 - 09:45:31 PDT)
[AMBER] Have any one used the Nmode to calculate the entropy?
Kong, Ren
(Thu Aug 09 2012 - 09:59:26 PDT)
Re: [AMBER] Have any one used the Nmode to calculate the entropy?
Jason Swails
(Thu Aug 09 2012 - 10:35:03 PDT)
Re: [AMBER] Have any one used the Nmode to calculate the entropy?
Matthew Tessier
(Thu Aug 09 2012 - 12:12:46 PDT)
Re: [AMBER] Have any one used the Nmode to calculate the entropy?
Matthew Tessier
(Mon Aug 20 2012 - 08:42:43 PDT)
[AMBER] How to save Eigenvectors of modes using MMPBSA.py script?
habi
(Thu Aug 09 2012 - 10:36:46 PDT)
[AMBER] How to recover box information from pdb with truncated octahedron solvent?
Liu Denis
(Thu Aug 09 2012 - 21:24:03 PDT)
[AMBER] Problem while using acdoctor command
Sumra Wajid Abbasi 30-FBAS/MSBI/F09
(Thu Aug 09 2012 - 23:09:15 PDT)
Re: [AMBER] Problem while using acdoctor command
David A Case
(Tue Aug 14 2012 - 05:30:01 PDT)
[AMBER] Errors during minimization (rfree: Error decoding variable 1 3)
Zalikha Ibrahim
(Fri Aug 10 2012 - 01:01:52 PDT)
Re: [AMBER] Errors during minimization (rfree: Error decoding variable 1 3)
Terry
(Fri Aug 10 2012 - 01:06:01 PDT)
Re: [AMBER] Errors during minimization (rfree: Error decoding variable 1 3)
Jason Swails
(Fri Aug 10 2012 - 05:40:15 PDT)
[AMBER] unique atom names
Chris Chris
(Fri Aug 10 2012 - 08:56:49 PDT)
Re: [AMBER] unique atom names
case
(Fri Aug 10 2012 - 17:54:37 PDT)
[AMBER] specific atom restraint
Thanh Binh NGUYEN
(Fri Aug 10 2012 - 09:09:47 PDT)
Re: [AMBER] specific atom restraint
Jason Swails
(Fri Aug 10 2012 - 10:04:38 PDT)
Re: [AMBER] specific atom restraint
Thanh Binh NGUYEN
(Fri Aug 10 2012 - 20:08:55 PDT)
[AMBER] Installation of Amber11
Meena Singh
(Sat Aug 11 2012 - 03:32:49 PDT)
Re: [AMBER] Installation of Amber11
case
(Sat Aug 11 2012 - 05:57:31 PDT)
[AMBER] Production md
ariana karakutuk
(Mon Aug 13 2012 - 03:06:04 PDT)
Re: [AMBER] Production md
case
(Mon Aug 13 2012 - 05:35:01 PDT)
Re: [AMBER] Production md
ariana karakutuk
(Tue Aug 14 2012 - 00:19:56 PDT)
Re: [AMBER] Production md
David A Case
(Tue Aug 14 2012 - 05:09:23 PDT)
Re: [AMBER] Production md
ariana karakutuk
(Thu Aug 16 2012 - 00:55:01 PDT)
Re: [AMBER] Production md
David A Case
(Thu Aug 16 2012 - 05:08:34 PDT)
[AMBER] Internal energy linear increase with temperature
Binwu Zhao
(Mon Aug 13 2012 - 08:01:19 PDT)
Re: [AMBER] Internal energy linear increase with temperature
David A Case
(Mon Aug 13 2012 - 08:16:19 PDT)
[AMBER] General question
George Tzotzos
(Mon Aug 13 2012 - 13:42:02 PDT)
Re: [AMBER] General question
Jason Swails
(Mon Aug 13 2012 - 19:08:01 PDT)
Re: [AMBER] General question
Gould, Ian R
(Tue Aug 14 2012 - 01:06:37 PDT)
Re: [AMBER] General question
George Tzotzos
(Tue Aug 14 2012 - 01:12:50 PDT)
[AMBER] Query about how to run ambertools12 after installing it
Yousef Elsyid
(Tue Aug 14 2012 - 05:04:38 PDT)
Re: [AMBER] Query about how to run ambertools12 after installing it
David A Case
(Tue Aug 14 2012 - 06:40:44 PDT)
[AMBER] RMS fit
Eliac Brown
(Tue Aug 14 2012 - 07:45:13 PDT)
Re: [AMBER] RMS fit
Daniel Roe
(Tue Aug 14 2012 - 08:04:10 PDT)
Re: [AMBER] RMS fit
Eliac Brown
(Tue Aug 14 2012 - 10:06:03 PDT)
Re: [AMBER] RMS fit
Jason Swails
(Tue Aug 14 2012 - 10:29:29 PDT)
Re: [AMBER] RMS fit
Daniel Roe
(Tue Aug 14 2012 - 10:35:30 PDT)
[AMBER] More RMS fit
George Tzotzos
(Thu Aug 23 2012 - 05:28:05 PDT)
[AMBER] RECALL More RMS fit
George Tzotzos
(Thu Aug 23 2012 - 05:34:47 PDT)
[AMBER] Problems when using cpptraj for reimaging when INPCRD file is one of the input frames
Marek Maly
(Tue Aug 14 2012 - 11:57:52 PDT)
Re: [AMBER] Problems when using cpptraj for reimaging when INPCRD file is one of the input frames
Daniel Roe
(Tue Aug 14 2012 - 15:30:33 PDT)
Re: [AMBER] Problems when using cpptraj for reimaging when INPCRD file is one of the input frames
Marek Maly
(Wed Aug 15 2012 - 03:11:31 PDT)
Re: [AMBER] Problems when using cpptraj for reimaging when INPCRD file is one of the input frames
Daniel Roe
(Wed Aug 15 2012 - 10:49:18 PDT)
Re: [AMBER] Problems when using cpptraj for reimaging when INPCRD file is one of the input frames
Marek Maly
(Wed Aug 15 2012 - 11:21:08 PDT)
Re: [AMBER] Problems when using cpptraj for reimaging when INPCRD file is one of the input frames
Daniel Roe
(Wed Aug 15 2012 - 12:55:50 PDT)
Re: [AMBER] Problems when using cpptraj for reimaging when INPCRD file is one of the input frames
Daniel Roe
(Wed Aug 15 2012 - 13:29:34 PDT)
Re: [AMBER] Problems when using cpptraj for reimaging when INPCRD file is one of the input frames
Marek Maly
(Wed Aug 15 2012 - 13:33:39 PDT)
Re: [AMBER] Problems when using cpptraj for reimaging when INPCRD file is one of the input frames
Daniel Roe
(Fri Aug 17 2012 - 06:58:21 PDT)
Re: [AMBER] Problems when using cpptraj for reimaging when INPCRD file is one of the input frames
Marek Maly
(Fri Aug 17 2012 - 06:59:57 PDT)
[AMBER] which part of source code implementing GB/SA simulations?
Xin Geng
(Tue Aug 14 2012 - 16:26:47 PDT)
Re: [AMBER] which part of source code implementing GB/SA simulations?
case
(Tue Aug 14 2012 - 19:30:49 PDT)
Re: [AMBER] which part of source code implementing GB/SA simulations?
Xin Geng
(Tue Aug 14 2012 - 20:48:24 PDT)
[AMBER] which part of source code implementing GB/SA simulations?
Xin Geng
(Tue Aug 14 2012 - 20:42:10 PDT)
[AMBER] job in multiple GPUs
Vijay Manickam Achari
(Tue Aug 14 2012 - 21:41:40 PDT)
[AMBER] Fatal error (Could not read velocities) during heating
Zalikha Ibrahim
(Wed Aug 15 2012 - 02:09:51 PDT)
Re: [AMBER] Fatal error (Could not read velocities) during heating
David A Case
(Wed Aug 15 2012 - 05:00:34 PDT)
Re: [AMBER] Fatal error (Could not read velocities) during heating
Jason Swails
(Wed Aug 15 2012 - 06:02:57 PDT)
[AMBER] Temperature regulation in HREMD
Brian Radak
(Wed Aug 15 2012 - 06:39:31 PDT)
Re: [AMBER] Temperature regulation in HREMD
dani sd
(Wed Aug 15 2012 - 11:39:59 PDT)
Re: [AMBER] Temperature regulation in HREMD
Carlos Simmerling
(Wed Aug 15 2012 - 12:58:45 PDT)
Re: [AMBER] Temperature regulation in HREMD
dani sd
(Wed Aug 15 2012 - 13:29:58 PDT)
[AMBER] PRMTOP TO PSF
manikanthan bhavaraju
(Wed Aug 15 2012 - 11:34:29 PDT)
Re: [AMBER] PRMTOP TO PSF
case
(Wed Aug 15 2012 - 18:16:09 PDT)
[AMBER] meaning of "tolerance" in REMD
Sajeewa Pemasinghe
(Wed Aug 15 2012 - 11:12:48 PDT)
[AMBER] Fwd: meaning of "tolerance" in REMD
Sajeewa Pemasinghe
(Thu Aug 16 2012 - 11:02:54 PDT)
Re: [AMBER] Fwd: meaning of "tolerance" in REMD
Brian Radak
(Thu Aug 16 2012 - 11:53:12 PDT)
Re: [AMBER] Fwd: meaning of "tolerance" in REMD
Sajeewa Pemasinghe
(Thu Aug 16 2012 - 14:38:43 PDT)
Re: [AMBER] Fwd: meaning of "tolerance" in REMD
Niel Henriksen
(Thu Aug 16 2012 - 14:46:53 PDT)
Re: [AMBER] Fwd: meaning of "tolerance" in REMD
Jason Swails
(Thu Aug 16 2012 - 15:56:07 PDT)
[AMBER] amber10 install
Qian Wang
(Wed Aug 15 2012 - 13:31:00 PDT)
Re: [AMBER] amber10 install
case
(Wed Aug 15 2012 - 18:22:58 PDT)
Re: [AMBER] amber10 install
Qian Wang
(Thu Aug 16 2012 - 07:18:40 PDT)
Re: [AMBER] amber10 install
David A Case
(Thu Aug 16 2012 - 07:25:40 PDT)
Re: [AMBER] amber10 install
Qian Wang
(Thu Aug 16 2012 - 07:33:16 PDT)
[AMBER] how to predict time for MMPBSA decomp analysis
vaibhav dixit
(Wed Aug 15 2012 - 22:45:23 PDT)
Re: [AMBER] how to predict time for MMPBSA decomp analysis
Jason Swails
(Thu Aug 16 2012 - 07:34:26 PDT)
Re: [AMBER] how to predict time for MMPBSA decomp analysis
vaibhav dixit
(Thu Aug 16 2012 - 08:59:49 PDT)
Re: [AMBER] how to predict time for MMPBSA decomp analysis
vaibhav dixit
(Mon Aug 20 2012 - 22:03:13 PDT)
Re: [AMBER] how to predict time for MMPBSA decomp analysis
Soumya Lipsa Rath
(Mon Aug 20 2012 - 22:57:54 PDT)
Re: [AMBER] how to predict time for MMPBSA decomp analysis
Jiri Sponer
(Tue Aug 21 2012 - 00:44:00 PDT)
[AMBER] MBAR calculation
Liu Denis
(Thu Aug 16 2012 - 08:33:21 PDT)
Re: [AMBER] MBAR calculation
Brian Radak
(Thu Aug 16 2012 - 08:50:57 PDT)
[AMBER] Help with ncsu_abmd flooding mode
Fabrício Bracht
(Thu Aug 16 2012 - 14:15:09 PDT)
[AMBER] Help with ncsu_abmd flooding mode
Fabrício Bracht
(Mon Aug 27 2012 - 08:17:00 PDT)
Re: [AMBER] Help with ncsu_abmd flooding mode
Brian Radak
(Mon Aug 27 2012 - 09:08:15 PDT)
Re: [AMBER] Help with ncsu_abmd flooding mode
Fabrício Bracht
(Mon Aug 27 2012 - 10:48:17 PDT)
Re: [AMBER] Help with ncsu_abmd flooding mode
Jason Swails
(Mon Aug 27 2012 - 11:16:26 PDT)
Re: [AMBER] Help with ncsu_abmd flooding mode
M. L. Dodson
(Mon Aug 27 2012 - 14:05:12 PDT)
[AMBER] Zn atom flying off
moitrayee.mbu.iisc.ernet.in
(Fri Aug 17 2012 - 06:55:18 PDT)
[AMBER] nmode - calculation of vibrational frequencies
Svetlana Oard
(Fri Aug 17 2012 - 09:04:33 PDT)
Re: [AMBER] nmode - calculation of vibrational frequencies
case
(Tue Aug 21 2012 - 18:39:40 PDT)
Re: [AMBER] nmode - calculation of vibrational frequencies
Svetlana Oard
(Thu Aug 23 2012 - 09:53:09 PDT)
[AMBER] Calculating Energy of an atom selection
Aron Broom
(Fri Aug 17 2012 - 14:19:28 PDT)
[AMBER] COM coordinates
Vishal Maingi
(Fri Aug 17 2012 - 15:57:38 PDT)
Re: [AMBER] COM coordinates
Vishal Maingi
(Tue Aug 21 2012 - 02:12:39 PDT)
Re: [AMBER] COM coordinates
Daniel Roe
(Tue Aug 21 2012 - 14:00:56 PDT)
Re: [AMBER] COM coordinates
Vishal Maingi
(Tue Aug 21 2012 - 23:59:25 PDT)
[AMBER] where is the subroutine amflsh in Amber10?
Xin Geng
(Sat Aug 18 2012 - 15:50:38 PDT)
Re: [AMBER] where is the subroutine amflsh in Amber10?
case
(Sun Aug 19 2012 - 06:08:00 PDT)
[AMBER] Flag for saving particular residues.
HIMANSHU JOSHI
(Sat Aug 18 2012 - 23:04:58 PDT)
Re: [AMBER] Flag for saving particular residues.
case
(Sun Aug 19 2012 - 08:18:01 PDT)
[AMBER] Error message in cpptraj when running at single node in supercomputer using mpirun
Catein Catherine
(Sun Aug 19 2012 - 18:53:31 PDT)
Re: [AMBER] Error message in cpptraj when running at single node in supercomputer using mpirun
Jason Swails
(Sun Aug 19 2012 - 21:07:09 PDT)
Re: [AMBER] Error message in cpptraj when running at single node in supercomputer using mpirun
Catein Catherine
(Sun Aug 19 2012 - 23:57:23 PDT)
Re: [AMBER] FW: Re: How to Calculate SASA with Amber?
E. Nihal Korkmaz
(Sun Aug 19 2012 - 20:49:25 PDT)
Re: [AMBER] FW: Re: How to Calculate SASA with Amber?
E. Nihal Korkmaz
(Sun Aug 19 2012 - 20:52:24 PDT)
Re: [AMBER] FW: Re: How to Calculate SASA with Amber?
Ross Walker
(Sun Aug 19 2012 - 20:58:49 PDT)
Re: [AMBER] FW: Re: How to Calculate SASA with Amber?
Jason Swails
(Sun Aug 19 2012 - 20:59:38 PDT)
Re: [AMBER] FW: Re: How to Calculate SASA with Amber?
Daniel Roe
(Sun Aug 19 2012 - 21:20:56 PDT)
[AMBER] Accelerated Molecular Dynamics in Amber12
Soumya Lipsa Rath
(Sun Aug 19 2012 - 22:15:11 PDT)
Re: [AMBER] Accelerated Molecular Dynamics in Amber12
Ross Walker
(Sun Aug 19 2012 - 23:06:13 PDT)
[AMBER] How to get the averaged structure of each cluster with cpptraj?
Catein Catherine
(Mon Aug 20 2012 - 00:01:14 PDT)
Re: [AMBER] How to get the averaged structure of each cluster with cpptraj?
Daniel Roe
(Mon Aug 20 2012 - 06:41:47 PDT)
Re: [AMBER] Accelerated Molecular Dynamics in Amber12
Soumya Lipsa Rath
(Mon Aug 20 2012 - 00:04:04 PDT)
Re: [AMBER] pbsa: how to increase the sampling volume (grid dimensions)?
Jan-Philip Gehrcke
(Mon Aug 20 2012 - 03:24:49 PDT)
Re: [AMBER] pbsa: how to increase the sampling volume (grid dimensions)?
Ray Luo
(Wed Aug 22 2012 - 07:25:49 PDT)
Re: [AMBER] Internal energy linear increase with temperature (David A Case)
Binwu Zhao
(Mon Aug 20 2012 - 12:56:02 PDT)
Re: [AMBER] Internal energy linear increase with temperature (David A Case)
David A Case
(Mon Aug 20 2012 - 13:40:43 PDT)
[AMBER] pmemd.cuda and nmropt
Larry Olson
(Mon Aug 20 2012 - 14:08:46 PDT)
Re: [AMBER] pmemd.cuda and nmropt
Ross Walker
(Mon Aug 20 2012 - 14:20:50 PDT)
[AMBER] transition metal system works on pmemd crashes on pmemd.cuda
Patrick von Glehn
(Mon Aug 20 2012 - 16:37:41 PDT)
Re: [AMBER] transition metal system works on pmemd crashes on pmemd.cuda
Scott Le Grand
(Mon Aug 20 2012 - 19:35:09 PDT)
Re: [AMBER] transition metal system works on pmemd crashes on pmemd.cuda
Patrick von Glehn
(Wed Aug 22 2012 - 07:28:50 PDT)
Re: [AMBER] transition metal system works on pmemd crashes on pmemd.cuda
Jason Swails
(Wed Aug 22 2012 - 07:50:05 PDT)
[AMBER] AMBER alanine scan with chlorine
Mannan
(Tue Aug 21 2012 - 02:31:50 PDT)
Re: [AMBER] AMBER alanine scan with chlorine
Bill Miller III
(Tue Aug 21 2012 - 04:04:28 PDT)
[AMBER] Recommendations for Amber on AMD Bulldozer
Jan-Philip Gehrcke
(Tue Aug 21 2012 - 05:02:52 PDT)
Re: [AMBER] Recommendations for Amber on AMD Bulldozer
Ross Walker
(Tue Aug 21 2012 - 07:56:49 PDT)
Re: [AMBER] Recommendations for Amber on AMD Bulldozer
Jan-Philip Gehrcke
(Tue Aug 21 2012 - 10:17:42 PDT)
[AMBER] amber10 install (mpi)
Qian Wang
(Tue Aug 21 2012 - 14:11:22 PDT)
Re: [AMBER] amber10 install (mpi)
Jason Swails
(Tue Aug 21 2012 - 14:18:50 PDT)
Re: [AMBER] amber10 install (mpi)
Qian Wang
(Tue Aug 21 2012 - 14:39:42 PDT)
Re: [AMBER] amber10 install (mpi)
Jason Swails
(Tue Aug 21 2012 - 15:05:40 PDT)
Re: [AMBER] amber10 install (mpi)
Qian Wang
(Tue Aug 21 2012 - 15:14:28 PDT)
Re: [AMBER] amber10 install (mpi)
Jason Swails
(Tue Aug 21 2012 - 16:20:43 PDT)
Re: [AMBER] amber10 install (mpi)
case
(Tue Aug 21 2012 - 18:26:47 PDT)
Re: [AMBER] amber10 install (mpi)
Qian Wang
(Wed Aug 22 2012 - 07:41:09 PDT)
[AMBER] area per lipid popc membrane
Fabrício Bracht
(Tue Aug 21 2012 - 14:25:28 PDT)
Re: [AMBER] area per lipid popc membrane
Benjamin D Madej
(Wed Aug 22 2012 - 10:51:37 PDT)
Re: [AMBER] area per lipid popc membrane
Fabrício Bracht
(Wed Aug 22 2012 - 15:39:26 PDT)
Re: [AMBER] area per lipid popc membrane
Benjamin D Madej
(Wed Aug 22 2012 - 16:20:55 PDT)
Re: [AMBER] area per lipid popc membrane
jojartb.jgypk.u-szeged.hu
(Wed Aug 22 2012 - 22:19:14 PDT)
Re: [AMBER] area per lipid popc membrane
Albert
(Wed Aug 22 2012 - 22:52:19 PDT)
Re: [AMBER] area per lipid popc membrane
Dickson, Callum
(Thu Aug 23 2012 - 02:12:14 PDT)
Re: [AMBER] MMPBSA.py gbsa unrecognized
E. Nihal Korkmaz
(Tue Aug 21 2012 - 21:19:33 PDT)
Re: [AMBER] MMPBSA.py gbsa unrecognized
Jason Swails
(Tue Aug 21 2012 - 21:44:32 PDT)
[AMBER] Is there any guide/tutorial/review to decide input format for MD based on system under consideration
vaibhav dixit
(Tue Aug 21 2012 - 22:46:34 PDT)
[AMBER] How to derive dihedral angle force constants by MCPB
JiYuan Liu
(Wed Aug 22 2012 - 01:20:28 PDT)
Re: [AMBER] How to derive dihedral angle force constants by MCPB
Ben Roberts
(Wed Aug 22 2012 - 15:50:15 PDT)
[AMBER] Diffenent EPB in MMPBSA result with
Liu Denis
(Wed Aug 22 2012 - 02:03:56 PDT)
Re: [AMBER] Diffenent EPB in MMPBSA result with
Liu Denis
(Wed Aug 22 2012 - 10:18:45 PDT)
Re: [AMBER] Diffenent EPB in MMPBSA result with
Miguel Ortiz Lombardia
(Wed Aug 22 2012 - 10:26:13 PDT)
Re: [AMBER] Diffenent EPB in MMPBSA result with
Qin Cai
(Thu Aug 23 2012 - 10:21:24 PDT)
Re: [AMBER] Diffenent EPB in MMPBSA result with
Qin Cai
(Fri Aug 31 2012 - 11:35:13 PDT)
[AMBER] NPT at high pressure
Francesco Pietra
(Wed Aug 22 2012 - 06:33:30 PDT)
Re: [AMBER] NPT at high pressure
Jason Swails
(Wed Aug 22 2012 - 07:19:46 PDT)
Re: [AMBER] NPT at high pressure
Francesco Pietra
(Wed Aug 22 2012 - 07:36:37 PDT)
[AMBER] Amber 12 cuda test suite: some tests 'hang'
Jan-Philip Gehrcke
(Wed Aug 22 2012 - 08:00:35 PDT)
Re: [AMBER] Amber 12 cuda test suite: some tests 'hang'
Ross Walker
(Wed Aug 22 2012 - 08:08:47 PDT)
Re: [AMBER] Amber 12 cuda test suite: some tests 'hang'
Jan-Philip Gehrcke
(Wed Aug 22 2012 - 08:25:47 PDT)
Re: [AMBER] Amber 12 cuda test suite: some tests 'hang'
Ross Walker
(Wed Aug 22 2012 - 09:04:14 PDT)
Re: [AMBER] Amber 12 cuda test suite: some tests 'hang'
Jan-Philip Gehrcke
(Wed Aug 22 2012 - 11:35:23 PDT)
Re: [AMBER] Amber 12 cuda test suite: some tests 'hang'
Ross Walker
(Wed Aug 22 2012 - 12:20:22 PDT)
Re: [AMBER] Amber 12 cuda test suite: some tests 'hang'
Jan-Philip Gehrcke
(Wed Aug 22 2012 - 14:11:31 PDT)
Re: [AMBER] Amber 12 cuda test suite: some tests 'hang'
Robert Crovella
(Fri Aug 24 2012 - 06:58:32 PDT)
Re: [AMBER] Amber 12 cuda test suite: some tests 'hang'
Scott Le Grand
(Wed Aug 22 2012 - 08:53:16 PDT)
Re: [AMBER] Amber 12 cuda test suite: some tests 'hang'
Jan-Philip Gehrcke
(Wed Aug 22 2012 - 08:57:02 PDT)
[AMBER] protein+DNA simulation
najmul arfin
(Wed Aug 22 2012 - 11:40:18 PDT)
Re: [AMBER] protein+DNA simulation
Thomas Cheatham III
(Wed Aug 22 2012 - 15:17:41 PDT)
Re: [AMBER] protein+DNA simulation
Dean Cuebas
(Thu Aug 23 2012 - 09:50:45 PDT)
[AMBER] Help about the igb
Elaine Cheung
(Wed Aug 22 2012 - 11:56:44 PDT)
Re: [AMBER] Help about the igb
Carlos Simmerling
(Wed Aug 22 2012 - 15:28:26 PDT)
Re: [AMBER] Help about the igb
Elaine Cheung
(Wed Aug 22 2012 - 18:51:39 PDT)
Re: [AMBER] Help about the igb
Carlos Simmerling
(Sat Aug 25 2012 - 04:55:27 PDT)
[AMBER] Can we use Ambertools analysis MD from GROMACS
Acoot Brett
(Mon Aug 27 2012 - 01:52:30 PDT)
Re: [AMBER] Can we use Ambertools analysis MD from GROMACS
Jason Swails
(Mon Aug 27 2012 - 04:02:25 PDT)
Re: [AMBER] Can we use Ambertools analysis MD from GROMACS
Pawel
(Mon Aug 27 2012 - 05:47:58 PDT)
Re: [AMBER] Help about the igb
Elaine Cheung
(Mon Aug 27 2012 - 08:22:50 PDT)
[AMBER] problem w/ radial results
E. Nihal Korkmaz
(Wed Aug 22 2012 - 14:23:04 PDT)
Re: [AMBER] problem w/ radial results
Thomas Cheatham III
(Wed Aug 22 2012 - 14:56:37 PDT)
[AMBER] loading of a mutant protein in XLEaP
gargi borgohai
(Wed Aug 22 2012 - 23:32:57 PDT)
Re: [AMBER] loading of a mutant protein in XLEaP
Jason Swails
(Thu Aug 23 2012 - 07:33:55 PDT)
[AMBER] ptraj: msd with diffusion command
Bala subramanian
(Thu Aug 23 2012 - 07:41:45 PDT)
Re: [AMBER] ptraj: msd with diffusion command
Daniel Roe
(Thu Aug 23 2012 - 12:09:58 PDT)
Re: [AMBER] ptraj: msd with diffusion command
Dmitry Mukha
(Sat Aug 25 2012 - 08:59:06 PDT)
Re: [AMBER] ptraj: msd with diffusion command
Bala subramanian
(Fri Aug 31 2012 - 10:47:14 PDT)
[AMBER] amber 12 installation error
Shuyi Cao
(Thu Aug 23 2012 - 09:04:22 PDT)
Re: [AMBER] amber 12 installation error
Jason Swails
(Thu Aug 23 2012 - 10:58:17 PDT)
[AMBER] failed to config serial amber 12 on IBM POWER7
Yubo Fan
(Thu Aug 23 2012 - 09:49:52 PDT)
[AMBER] Different Properties Value with Tesla vs GeForce GPUs
Ismail, Mohd F.
(Thu Aug 23 2012 - 10:40:50 PDT)
[AMBER] AMBER Workshop Announcement - Oct 8th to 12th - Lausanne Switzerland
Ross Walker
(Thu Aug 23 2012 - 11:05:14 PDT)
Re: [AMBER] AMBER Workshop Announcement - Oct 8th to 12th - Lausanne Switzerland
Albert
(Thu Aug 23 2012 - 11:08:16 PDT)
Re: [AMBER] AMBER Workshop Announcement - Oct 8th to 12th - Lausanne Switzerland
Ross Walker
(Thu Aug 23 2012 - 11:16:35 PDT)
Re: [AMBER] AMBER Workshop Announcement - Oct 8th to 12th - Lausanne Switzerland
Albert
(Fri Aug 24 2012 - 01:47:01 PDT)
[AMBER] parallel installation problem: Amber11+AmberTools1.4 on a linux cluster
Alfred Zheng
(Thu Aug 23 2012 - 17:14:00 PDT)
Re: [AMBER] parallel installation problem: Amber11+AmberTools1.4 on a linux cluster
Jason Swails
(Thu Aug 23 2012 - 18:08:05 PDT)
[AMBER] about ions
Carlos Romero
(Thu Aug 23 2012 - 22:50:34 PDT)
Re: [AMBER] about ions
David A Case
(Fri Aug 24 2012 - 05:52:28 PDT)
Re: [AMBER] about ions
Carlos Romero
(Fri Aug 24 2012 - 17:44:37 PDT)
Re: [AMBER] about ions
Jason Swails
(Fri Aug 24 2012 - 19:57:04 PDT)
Re: [AMBER] about ions
Carlos Romero
(Sun Aug 26 2012 - 16:55:19 PDT)
[AMBER] failed to config serial amber 12 on IBM POWER7
Yubo Fan
(Thu Aug 23 2012 - 23:40:45 PDT)
Re: [AMBER] failed to config serial amber 12 on IBM POWER7
David A Case
(Fri Aug 24 2012 - 06:09:10 PDT)
[AMBER] cpptraj surf
George Tzotzos
(Fri Aug 24 2012 - 06:22:01 PDT)
Re: [AMBER] cpptraj surf
Daniel Roe
(Fri Aug 24 2012 - 07:37:37 PDT)
Re: [AMBER] cpptraj surf
George Tzotzos
(Fri Aug 24 2012 - 08:28:55 PDT)
Re: [AMBER] cpptraj surf
Jason Swails
(Fri Aug 24 2012 - 08:47:59 PDT)
Re: [AMBER] cpptraj surf
George Tzotzos
(Fri Aug 24 2012 - 09:21:22 PDT)
Re: [AMBER] cpptraj surf
Daniel Roe
(Fri Aug 24 2012 - 09:32:36 PDT)
Re: [AMBER] cpptraj surf
George Tzotzos
(Fri Aug 24 2012 - 09:52:46 PDT)
Re: [AMBER] cpptraj surf
Jason Swails
(Fri Aug 24 2012 - 10:42:25 PDT)
[AMBER] CPPTRAJ: Is it a program that requires a large memory?
Catein Catherine
(Mon Aug 27 2012 - 00:06:42 PDT)
Re: [AMBER] CPPTRAJ: Is it a program that requires a large memory?
Jason Swails
(Mon Aug 27 2012 - 03:59:52 PDT)
Re: [AMBER] CPPTRAJ: Is it a program that requires a large memory?
Daniel Roe
(Mon Aug 27 2012 - 18:02:21 PDT)
[AMBER] parallel constraints SMD
e g
(Fri Aug 24 2012 - 08:39:59 PDT)
Re: [AMBER] parallel constraints SMD
Jason Swails
(Fri Aug 24 2012 - 08:51:19 PDT)
Re: [AMBER] parallel constraints SMD
e g
(Fri Aug 24 2012 - 12:38:03 PDT)
[AMBER] Can electrostatic potential of GBSA be visualized?
Liu Denis
(Sat Aug 25 2012 - 06:28:49 PDT)
[AMBER] parallel run error
najmul arfin
(Sun Aug 26 2012 - 22:04:43 PDT)
Re: [AMBER] parallel run error
Jason Swails
(Mon Aug 27 2012 - 03:52:14 PDT)
[AMBER] Decomposing the free energy contributions to the binding free energy
Deák Robert
(Mon Aug 27 2012 - 00:55:17 PDT)
Re: [AMBER] Decomposing the free energy contributions to the binding free energy
Liu Denis
(Mon Aug 27 2012 - 09:47:12 PDT)
Re: [AMBER] Decomposing the free energy contributions to the binding free energy
Deák Robert
(Mon Aug 27 2012 - 12:52:12 PDT)
Re: [AMBER] Decomposing the free energy contributions to the binding free energy
Liu Denis
(Mon Aug 27 2012 - 17:51:39 PDT)
Re: [AMBER] Decomposing the free energy contributions to the binding free energy
Deák Robert
(Tue Aug 28 2012 - 03:12:03 PDT)
Re: [AMBER] Decomposing the free energy contributions to the binding free energy
Jason Swails
(Tue Aug 28 2012 - 07:05:19 PDT)
[AMBER] GDP and MG parameters
Vlad Cojocaru
(Mon Aug 27 2012 - 01:21:56 PDT)
Re: [AMBER] GDP and MG parameters
George M Giambasu
(Mon Aug 27 2012 - 09:40:18 PDT)
Re: [AMBER] GDP and MG parameters
FyD
(Tue Aug 28 2012 - 03:15:54 PDT)
Re: [AMBER] GDP and MG parameters
Vlad Cojocaru
(Tue Aug 28 2012 - 04:09:22 PDT)
Re: [AMBER] GDP and MG parameters
FyD
(Tue Aug 28 2012 - 09:17:17 PDT)
Re: [AMBER] GDP and MG parameters
Vlad Cojocaru
(Tue Aug 28 2012 - 11:42:22 PDT)
[AMBER] Particles diffuse very far away from each other
ariana karakutuk
(Mon Aug 27 2012 - 22:11:07 PDT)
Re: [AMBER] Particles diffuse very far away from each other
Jason Swails
(Mon Aug 27 2012 - 23:12:40 PDT)
[AMBER] help about TMD
燕燕朱
(Tue Aug 28 2012 - 05:10:49 PDT)
Re: [AMBER] help about TMD
David A Case
(Tue Aug 28 2012 - 06:19:25 PDT)
[AMBER] How can I get a average structure?
Sanjib Paul
(Tue Aug 28 2012 - 07:05:47 PDT)
Re: [AMBER] How can I get a average structure?
Jason Swails
(Tue Aug 28 2012 - 07:13:18 PDT)
[AMBER] Can we use autoimage of cpptraj in AMBER 12?
Catein Catherine
(Tue Aug 28 2012 - 07:31:14 PDT)
Re: [AMBER] Can we use autoimage of cpptraj in AMBER 12?
Jason Swails
(Tue Aug 28 2012 - 07:41:25 PDT)
Re: [AMBER] How can I get a average structure?
Sanjib Paul
(Tue Aug 28 2012 - 08:33:41 PDT)
Re: [AMBER] How can I get a average structure?
Daniel Roe
(Tue Aug 28 2012 - 09:12:52 PDT)
Re: [AMBER] How can I get a average structure?
Sanjib Paul
(Tue Aug 28 2012 - 09:39:24 PDT)
[AMBER] Dummy atom and PMEMD
Ali M. Naserian-Nik
(Tue Aug 28 2012 - 07:21:57 PDT)
Re: [AMBER] Dummy atom and PMEMD
case
(Tue Aug 28 2012 - 17:35:08 PDT)
Re: [AMBER] Dummy atom and PMEMD
Ali M. Naserian-Nik
(Tue Aug 28 2012 - 22:57:06 PDT)
Re: [AMBER] Dummy atom and PMEMD
David A Case
(Thu Aug 30 2012 - 10:04:53 PDT)
Re: [AMBER] Dummy atom and PMEMD
Ali M. Naserian-Nik
(Thu Aug 30 2012 - 11:29:31 PDT)
Re: [AMBER] Dummy atom and PMEMD
Jason Swails
(Thu Aug 30 2012 - 11:48:05 PDT)
Re: [AMBER] Dummy atom and PMEMD
Ali M. Naserian-Nik
(Thu Aug 30 2012 - 12:21:08 PDT)
Re: [AMBER] Dummy atom and PMEMD
Jason Swails
(Thu Aug 30 2012 - 13:05:11 PDT)
Re: [AMBER] Dummy atom and PMEMD
Ali M. Naserian-Nik
(Fri Aug 31 2012 - 00:20:57 PDT)
Re: [AMBER] Dummy atom and PMEMD
David A Case
(Fri Aug 31 2012 - 05:08:45 PDT)
[AMBER] Problem regarding imin = 5
Sanjib Paul
(Tue Aug 28 2012 - 10:50:09 PDT)
Re: [AMBER] Problem regarding imin = 5
Carlos Simmerling
(Tue Aug 28 2012 - 10:53:35 PDT)
Re: [AMBER] Problem regarding imin = 5
Sanjib Paul
(Tue Aug 28 2012 - 10:54:09 PDT)
Re: [AMBER] Problem regarding imin = 5
Sanjib Paul
(Tue Aug 28 2012 - 10:56:54 PDT)
[AMBER] MPI version of Amber on CPU provide different results in each run
Mohammad Ashraf Bhuiyan
(Tue Aug 28 2012 - 16:46:47 PDT)
Re: [AMBER] MPI version of Amber on CPU provide different results in each run
Liu Denis
(Tue Aug 28 2012 - 18:02:05 PDT)
[AMBER] "QMMM of protein-ligand complex: Unable to achieve self consistency" and "bond stretch too far"
psu4.uic.edu
(Tue Aug 28 2012 - 16:48:31 PDT)
[AMBER] Adding water molecules directly into files
Adam Jion
(Tue Aug 28 2012 - 21:04:15 PDT)
Re: [AMBER] Adding water molecules directly into files
Liu Denis
(Tue Aug 28 2012 - 21:10:00 PDT)
Re: [AMBER] Adding water molecules directly into files
Jason Swails
(Tue Aug 28 2012 - 21:24:58 PDT)
[AMBER] How to combine RMSF profiles?
Catein Catherine
(Tue Aug 28 2012 - 22:49:05 PDT)
Re: [AMBER] How to combine RMSF profiles?
Jason Swails
(Wed Aug 29 2012 - 07:38:46 PDT)
Re: [AMBER] How to combine RMSF profiles?
Catein Catherine
(Wed Aug 29 2012 - 20:10:43 PDT)
Re: [AMBER] How to combine RMSF profiles?
Jason Swails
(Wed Aug 29 2012 - 21:48:56 PDT)
Re: [AMBER] How to combine RMSF profiles?
Carlos Simmerling
(Wed Aug 29 2012 - 07:48:11 PDT)
Re: [AMBER] Adding water molecules directly into files
Marc van der Kamp
(Wed Aug 29 2012 - 01:40:29 PDT)
[AMBER] mpi4py import error mesage is improvable
Jan-Philip Gehrcke
(Wed Aug 29 2012 - 02:20:46 PDT)
Re: [AMBER] mpi4py import error mesage is improvable
Jason Swails
(Wed Aug 29 2012 - 07:25:28 PDT)
[AMBER] Amber 12: CalcError in mmpbsa_py_energy and sander
Jan-Philip Gehrcke
(Wed Aug 29 2012 - 05:11:28 PDT)
Re: [AMBER] Amber 12: CalcError in mmpbsa_py_energy and sander
Jason Swails
(Wed Aug 29 2012 - 07:17:17 PDT)
Re: [AMBER] Amber 12: CalcError in mmpbsa_py_energy and sander
Jan-Philip Gehrcke
(Fri Aug 31 2012 - 06:50:32 PDT)
Re: [AMBER] Amber 12: CalcError in mmpbsa_py_energy and sander
Jason Swails
(Fri Aug 31 2012 - 07:26:01 PDT)
Re: [AMBER] Amber 12: CalcError in mmpbsa_py_energy and sander
Jan-Philip Gehrcke
(Fri Aug 31 2012 - 07:58:31 PDT)
Re: [AMBER] Amber 12: CalcError in mmpbsa_py_energy and sander
Jason Swails
(Fri Aug 31 2012 - 08:43:24 PDT)
Re: [AMBER] Amber 12: CalcError in mmpbsa_py_energy and sander
Jan-Philip Gehrcke
(Fri Aug 31 2012 - 08:56:49 PDT)
Re: [AMBER] Amber 12: CalcError in mmpbsa_py_energy and sander
Ray Luo, Ph.D.
(Fri Aug 31 2012 - 09:55:12 PDT)
[AMBER] problem to perform nmode analysis
Sanjib Paul
(Wed Aug 29 2012 - 05:41:06 PDT)
Re: [AMBER] problem to perform nmode analysis
Sanjib Paul
(Wed Aug 29 2012 - 05:57:21 PDT)
Re: [AMBER] problem to perform nmode analysis
David A Case
(Wed Aug 29 2012 - 08:03:32 PDT)
Re: [AMBER] problem to perform nmode analysis
Jason Swails
(Wed Aug 29 2012 - 08:28:18 PDT)
Re: [AMBER] problem to perform nmode analysis
Sanjib Paul
(Wed Aug 29 2012 - 08:39:33 PDT)
[AMBER] CPPTRAJ hbond command
Samuel Genheden
(Wed Aug 29 2012 - 07:35:01 PDT)
Re: [AMBER] CPPTRAJ hbond command
Daniel Roe
(Wed Aug 29 2012 - 09:50:32 PDT)
[AMBER] group specification for different force constants for different groups
Sajeewa Pemasinghe
(Wed Aug 29 2012 - 10:06:36 PDT)
Re: [AMBER] group specification for different force constants for different groups
Jason Swails
(Wed Aug 29 2012 - 10:41:09 PDT)
[AMBER] keeping parts of a protein virtually frozen in MD with pmemd
Sajeewa Pemasinghe
(Wed Aug 29 2012 - 11:28:53 PDT)
[AMBER] Amber12 Configuring NetCDF or fftw3 or MTK++ hang
Yu Chen
(Wed Aug 29 2012 - 13:26:56 PDT)
Re: [AMBER] Amber12 Configuring NetCDF or fftw3 or MTK++ hang
Jason Swails
(Wed Aug 29 2012 - 14:16:21 PDT)
Re: [AMBER] Amber12 Configuring NetCDF or fftw3 or MTK++ hang
Ben Roberts
(Wed Aug 29 2012 - 15:54:50 PDT)
Re: [AMBER] Amber12 Configuring NetCDF or fftw3 or MTK++ hang
Yu Chen
(Thu Aug 30 2012 - 08:19:17 PDT)
Re: [AMBER] Amber12 Configuring NetCDF or fftw3 or MTK++ hang
Jason Swails
(Thu Aug 30 2012 - 08:29:34 PDT)
[AMBER] Installation problem of AmberTools of AMBER11
Sanjib Paul
(Wed Aug 29 2012 - 23:01:30 PDT)
Re: [AMBER] Installation problem of AmberTools of AMBER11
David A Case
(Thu Aug 30 2012 - 05:16:47 PDT)
Re: [AMBER] Installation problem of AmberTools of AMBER11
Sanjib Paul
(Thu Aug 30 2012 - 06:17:47 PDT)
Re: [AMBER] Installation problem of AmberTools of AMBER11
Jason Swails
(Thu Aug 30 2012 - 07:34:55 PDT)
Re: [AMBER] Installation problem of AmberTools of AMBER11
Sanjib Paul
(Thu Aug 30 2012 - 09:33:45 PDT)
Re: [AMBER] Installation problem of AmberTools of AMBER11
Jason Swails
(Thu Aug 30 2012 - 10:10:28 PDT)
Re: [AMBER] Installation problem of AmberTools of AMBER11
Sanjib Paul
(Thu Aug 30 2012 - 11:58:38 PDT)
Re: [AMBER] Installation problem of AmberTools of AMBER11
Jason Swails
(Thu Aug 30 2012 - 13:03:27 PDT)
Re: [AMBER] Installation problem of AmberTools of AMBER11
Sanjib Paul
(Thu Aug 30 2012 - 21:43:04 PDT)
Re: [AMBER] Installation problem of AmberTools of AMBER11
David A Case
(Fri Aug 31 2012 - 05:13:18 PDT)
[AMBER] Bacteriochlorophyll parameters from Ceccarelli et al.?
Marc van der Kamp
(Thu Aug 30 2012 - 08:33:32 PDT)
[AMBER] RESP charge derivation
shomesankar bhunia
(Thu Aug 30 2012 - 11:49:34 PDT)
Re: [AMBER] RESP charge derivation
Jason Swails
(Thu Aug 30 2012 - 11:55:57 PDT)
Re: [AMBER] RESP charge derivation
shomesankar bhunia
(Thu Aug 30 2012 - 12:04:44 PDT)
Re: [AMBER] RESP charge derivation
Jason Swails
(Thu Aug 30 2012 - 12:21:56 PDT)
Re: [AMBER] RESP charge derivation
shomesankar bhunia
(Thu Aug 30 2012 - 21:02:45 PDT)
Re: [AMBER] RESP charge derivation
shomesankar bhunia
(Thu Aug 30 2012 - 22:51:40 PDT)
Re: [AMBER] RESP charge derivation
FyD
(Thu Aug 30 2012 - 23:06:10 PDT)
Re: [AMBER] RESP charge derivation
shomesankar bhunia
(Thu Aug 30 2012 - 23:13:53 PDT)
[AMBER] Segmentation Fault in Tleap
Deepak Ojha
(Thu Aug 30 2012 - 14:19:37 PDT)
Re: [AMBER] Segmentation Fault in Tleap
Jason Swails
(Thu Aug 30 2012 - 16:52:28 PDT)
[AMBER] ions concenration
Carlos Romero
(Thu Aug 30 2012 - 18:30:17 PDT)
Re: [AMBER] ions concenration
Daniel Sindhikara
(Fri Aug 31 2012 - 07:32:39 PDT)
Re: [AMBER] ions concenration
Marek Maly
(Fri Aug 31 2012 - 08:07:43 PDT)
Re: [AMBER] ions concenration
Carlos Romero
(Fri Aug 31 2012 - 10:13:16 PDT)
Re: [AMBER] ions concenration
Carlos Romero
(Fri Aug 31 2012 - 08:40:00 PDT)
[AMBER] How to choose a particular region to minimization?
Thanh Binh NGUYEN
(Thu Aug 30 2012 - 23:55:02 PDT)
Re: [AMBER] How to choose a particular region to minimization?
Marc van der Kamp
(Fri Aug 31 2012 - 03:49:06 PDT)
Re: [AMBER] How to choose a particular region to minimization?
Thanh Binh NGUYEN
(Fri Aug 31 2012 - 04:09:50 PDT)
Re: [AMBER] How to choose a particular region to minimization?
Jason Swails
(Fri Aug 31 2012 - 07:31:26 PDT)
[AMBER] newbie question: simulating miRNA
Michiel de Hoon
(Fri Aug 31 2012 - 07:30:25 PDT)
Re: [AMBER] newbie question: simulating miRNA
Niel Henriksen
(Fri Aug 31 2012 - 08:47:10 PDT)
Re: [AMBER] newbie question: simulating miRNA
David A Case
(Fri Aug 31 2012 - 12:44:25 PDT)
Re: [AMBER] newbie question: simulating miRNA
Niel Henriksen
(Fri Aug 31 2012 - 12:53:59 PDT)
[AMBER] ERROR: max pairlist cutoff must be less than unit cell max sphere radius!
Gabriel Jara
(Fri Aug 31 2012 - 07:39:51 PDT)
Re: [AMBER] ERROR: max pairlist cutoff must be less than unit cell max sphere radius!
Brian Radak
(Fri Aug 31 2012 - 07:50:06 PDT)
Re: [AMBER] ERROR: max pairlist cutoff must be less than unit cell max sphere radius!
Gabriel Jara
(Fri Aug 31 2012 - 13:50:14 PDT)
Re: [AMBER] ERROR: max pairlist cutoff must be less than unit cell max sphere radius!
case
(Fri Aug 31 2012 - 15:38:57 PDT)
Last message date
:
Fri Aug 31 2012 - 16:00:03 PDT
Archived on
: Fri Apr 26 2024 - 05:54:41 PDT
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