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