AMBER Archive (2005) - Jan 2005 By Subject309 messages sorted by:
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Starting: Sat Jan 01 2005 - 08:08:24 CST
Ending: Mon Jan 31 2005 - 23:14:47 CST
- amber 8 problem
- AMBER: &dipoles in sander
- AMBER: .dat and frcmod files
- AMBER: about install amber8 on windows
- AMBER: amber 8 benchmarks dec alpha
- AMBER: amber 8 installation
- AMBER: amber 8 problem
- AMBER: AMBER 8: Freeze AND restrain questions
- AMBER: AMBER related employment
- AMBER: AMBER tutorial ambpdb question
- AMBER: amber8 in IBM-SP4
- AMBER: Amber8 installation problems on Sparc/Solaris9
- AMBER: amber8 parallel sander
- AMBER: AMBER8: compiling under cygwin using lahey fortran
- AMBER: Andersen thermostat: target T?
- AMBER: ANTECHAMBER & DIVCON
- AMBER: antechamber error message
- AMBER: calculating electrostatic potential
- AMBER: Can someone recommend a tutorial?
- AMBER: carnal - water-mediated HBond
- AMBER: collision frequency in GBSA dynamics
- AMBER: Compiling AMBER 8 for Mac OSX (Parallel)
- AMBER: Converting prmtop and inpcrd files
- AMBER: Coordinate Superimposition in PTRAJ
- AMBER: Copper library?
- AMBER: Cutoff for anal
- AMBER: D-amino acid prep-files(simple method)
- AMBER: details of new aminoacid
- AMBER: distance between images
- AMBER: distance restraint and file fort.35
- AMBER: Dummy Atoms: How to create them?
- AMBER: dynamics
- AMBER: eedmeth=5
- AMBER: enhanced sampling methods
- AMBER: error in parallel
- AMBER: Error while running resp.
- AMBER: Floating Exception and installation on Digital Unix.
- AMBER: Floating Exception in sander
- AMBER: gaussian output file
- AMBER: GB differences between AMBER7 and AMBER8
- AMBER: General Question about AMBER's Free Energy Perturbation Method
- AMBER: gold atoms
- AMBER: guanidinium chloride
- AMBER: H-atom types attached to a carbon atom next to carbonyl group
- AMBER: Hbonds restraints OK but Dihedral restraints not applied
- AMBER: How can i use AMBER with CHARMM forcefield parameter?
- AMBER: How to make PDB file by myself
- AMBER: How to set AMBER parameter files for lipid?
- AMBER: how to solvate in TIP5P box
- AMBER: IGB parameter
- AMBER: Increasing Volume with ntb=1
- AMBER: istart2
- AMBER: last call for early registrations for "Horizons2005"
- AMBER: LEAP
- AMBER: lipid bilayer membrane force field parameter
- AMBER: lipid parameter file
- AMBER: Manuals need update: protonate -b and -c options gone in Amber 7 and 8
- AMBER: MM_PBSA arguments for MM calculations
- AMBER: mm_pbsa example doesn't run
- AMBER: MM_PBSA fillratio error
- AMBER: N Metyl amino acids
- AMBER: NAN errors
- AMBER: NCOPY definition
- AMBER: new aminoacid
- AMBER: new tutorial available
- AMBER: nmode calculation
- AMBER: NSCM
- AMBER: parallel run
- AMBER: parametrization problem
- AMBER: PB dynamics
- AMBER: PBCAL=0. Problems in MM/PBSA
- AMBER: PBSA residual and pairwise decompostion
- AMBER: plane definition in ptraj
- AMBER: pmemd and distance restraint
- AMBER: pmemd and restraints
- AMBER: Problem in ptraj
- AMBER: problem runing parallel (REM) on tru64
- AMBER: Problem with computing Resp charges using RED
- AMBER: problem with position restraints (refc file)
- AMBER: problem with pressure equilibration
- AMBER: Problem with restart file
- AMBER: Problems with xLEaP
- AMBER: protonate
- AMBER: ptraj analysis
- AMBER: pucker: deatails about pucker calculation
- AMBER: QM/MM with pmemd
- AMBER: Question about TI integral method
- AMBER: question about xwin load pdb file
- AMBER: Questions about sander.QMMM
- AMBER: recompiling problem on IBM aix
- AMBER: replica exchange trouble with unit 6
- AMBER: RMS fluctuations along modes obtained from PCA
- AMBER: Sander and NMODE energy minimization
- AMBER: sander failure
- AMBER: sander free energy calculation
- AMBER: Sander Replica Exchange exits with unit 6 error
- AMBER: Sander Replica Exchange exits with unit 6 error]
- AMBER: Scaling of charges in a polarizable simulation !
- AMBER: skip snapshots with ptraj in amber 8.0
- AMBER: SO4 prep file
- AMBER: some question about MM-PBSA
- AMBER: Steered Molecular Dynamics with AMBER?
- AMBER: sugar pucker with Carnal and ptraj
- AMBER: Suspended (tty input)
- AMBER: system size limit
- AMBER: test suite possible failures
- AMBER: the DNA conformation after engery minimization using NMODE
- AMBER: TI with electrostatic decoupling at sander
- AMBER: units
- AMBER: van der waals parameters
- AMBER: Weighting of different restraint types?
- AMBER: What does a crash mean while running a md simulation?
- AMBER:Hydroxy Proline
- AMBER:idecomp
Last message date: Sat Dec 31 2005 - 12:51:27 CST
Archived on: Sat Dec 31 2005 - 12:51:45 CST
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