NAMD-L: By Subject
By Subject
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About this archive
Starting: Mon Sep 08 2003 - 09:54:14 CDT
Ending: Sun Jul 06 2008 - 07:51:49 CDT
- "Adaptive" force direction in SMD?
- "atoms moving too fast" error in bilayer simulation
- "binaryoutput no" doesn't work
- "Constrain failure" in NAMD
- "CWeb performance data sent to wrong processor..."
- "GRADIENT TOLERANCE: nan", Why?
- "Hands-On" Workshop on Computational Biophysics
- "make" Linux-amd64-g++ error
- "measure" command
- "Not all atoms have unique coordinates"
- "reinitvel" parameter in config file
- "RESTARTING CONJUGATE GRADIENT ALGORITHM"
- "Segmentation violation" on running namd2.6b1
- "Timeout waiting for node-program to connect" error, only sometimes
- "Unknown pragma ivdep and pragma vector" errors when compiling on BlueGene
- "wrapAll on" with a complex
- # of processors
- #QNAN: Please help!
- (no subject)
- *** topology file for AMP? ***
- ***** SPAM POSSIBLE ***** Warning: Not all atoms have unique coordinates.
- *.dcd and *.dcd.BAK
- , Build your vocab (word power)-Get emails daily Fr.ee
- ,log and .out files with namd running on mac os x (panther)
- ------------- Processor 0 Exiting: Called CmiAbort ------------
- .psf and .params files for IMD
- .xsc file and .restart.xsc file
- 0 coordinates for LES atoms in pdb file after solvation
- 1 D Periodic Boundary
- 1-4 interactions scaling
- 128+ proccessor jobs on 64bit Widows hang upon completion of the simulation.
- 1QSU
- 2 dimension PBC
- 2 domains rigid body rotation with IMD
- 2 molecule pair interactions
- 2 pdb files
- 2 proteins
- 2-D periodic boundary condition
- 2.6b1 source missing file
- 2D Ewald summation
- 2D periodic boundary condn & PME
- 32 vs. 64 bits
- 4th Annual Workshop on Charm++ and its Applications 2005
- 64 bit G5 plans for NAMD
- 64 bit NAMD on AIX and CatDCD
- 64 nodes behaviour
- <no subject>
- =20=20How=20to=20compile=20NAMD?= 2.6 on core2 operons, x86_64-redhat-linux,which isqthe=20proper=20choice=20in=20Arch.?=
- =20=20nodelist=20being=20ignore?= d during paralleling
- =20?= qHow=20to=20compile=20NAMD2.6=20on=20core2=20operons,=20x86=5F?= 64-redhat-linux,which is the proper choice in Arch .?=
- =20?= qhow=20to=20constrain=20a=20dihedral=20angle=3F?=
- =20How=20to=20build=20charm++=20on=20c?= ore2 processor
- > 10000 ato
- > 10000 atoms
- [Fwd: counterion software]
- [Fwd: HD speed ??]
- [Fwd: increasing RMSD after 2 ns minimization-equilibration]
- [Fwd: SMD of titin domain]
- [Fwd: Specific Heat Calculation with VMD]
- [Fwd: total energy stuck between two levels]
- [Periodic Boundary]: from charmm to namd
- _alloca undefined symbol (OS X/XL compiler)
- _NAMD_crashes?= on winx64 during parallel run.
- a basic question
- A basic question?
- A confused question on amber param and in charmm form~
- a different bug alert
- A difficult problem to explain the SMD force difference
- a display problem
- a error during install charm-5.9
- a name quesiton
- a philosophical question...
- A possibel wrong coding in Parameters::read_charmm_parameter_file(char *)
- A problem with intermediate files
- A puzzling problem about adsorption energy in solution.
- a question about equilibrium
- A question about MD simulation of peptide.
- A question about restaints force.
- A question about RMSD calculation
- A question on minimization
- A question on psfgen
- A question on simulation with NPT ensemble
- A question regarding generate pdb and psf file
- A serious problem of NAMD output.
- A strange phenomenon in my dynamics system,any suggestion?
- A strange thing about psfgen~
- a target molecule in a water box.
- A tool to set up alchemical FEP transformations
- a topology file in VMD
- abf
- abf "force not a vector" error
- ABF (fwd)
- ABF - changing the reaction coordinate
- ABF - PMF Calculation
- ABF - restricting reaction coordinate
- ABF - stretching deca-alanine
- ABF - zCoord for more than one monomer
- abf - zeros as output
- ABF : dihedral-com.tcl
- abf and tcl scripting in NAMD
- ABF application
- ABF calculations
- ABF error calculation
- ABF for conformational analysis
- ABF fullsamples
- ABF inFiles
- ABF Method
- ABF on a single molecule
- ABF or SMD
- abf output
- ABF Output File
- ABF parameters
- ABF question
- ABF restrain
- ABF Simulation
- ABF tutorial; updated FEP tutorial
- ABF using distance-com but with negative xiMin
- ABF with different bin size
- ABF with z-coord
- ABF.TCl file ???
- ABF: example works now; more questions.
- ABF: example works; more questions.
- abf: multiple distance
- ABF: split reaction coordinate in widows
- ABF:reversibility and number of samples
- About "get z" command in MD script language.
- About "mutate" command in psfgen package.
- about 'loadforces' command...help!
- about *.psf
- about abf
- About ADP
- About Amber force fields
- About calculating RMSD with rmsd.tcl
- About charm++/namd on AMD64 cluster
- About CHARMM charge
- about charmm topology file
- about counterions
- About cutoff parameter for real space calculation in PME
- about delta-G in PMF calculation
- about diahedra entry in top_all22_sugar.inp
- about ExcludeFromPressure
- about guesscoord
- about HIS residue
- about internal coordinate IC statement of CHARMM force field
- About ions Representation in NAMD
- About Langevin Damping Coefficient.
- About Langevin Dynamics.
- About loadcoors -- is there a loadvelocity?
- about MCTI output
- about membrane protein
- about normal mode analisys
- About para file format
- About PDB file with fixed atom flags.
- About pmf
- about PMF and MCTI
- About Potential Addition in NAMD
- About pressureProfile command for non-equilibrium system.
- about protonation of HIS in membrane protein
- about psf file
- About QM-MM
- About ref frame for rmsd vs time
- About Restart
- About restart.vel.old file.
- about rigid bonds
- About RMSD
- About RMSD calculation.
- about signal 11 received,exiting
- About smd
- about symmetry operations
- about TCL boundary forces
- about temperature reassign?
- About the command "loadtotalforces"
- About the command "set z [lindex $coorList($i) 2]".
- About the error of "Tcl interface"
- About the module of "External Electric Field "
- about the MSE residue
- About the potantial of IONS
- About the potential of NAMD
- About the SMD output file
- About the Source code.
- About the unit of "efield"
- about this bug alert
- About timestep again.
- About timestep again. -- Fastest motion O-H streching period 10 fs.
- about topology generation
- abrupt deviation in rmsd values
- ABSOLUTE IMPRECISION and RELATIVE IMPRECISION IN TABLE FORCE
- Accelerating groups of atoms
- Acceptable pressure values
- Accepted temperature and pressure oscillation
- Accessing beta / occupancy values from NAMD tcl
- ACE patch
- Acetaldehyde Dihedral Parameters
- AcetylProlineAmide topology
- across the nodes, namd jobs don't get enough CPU!
- add calcium chloride
- add ions
- add Mg2+
- add water on the top of the protein border
- added more bases to DNA using psfgen
- addforce
- Adding amino acids to an existing pdb structure
- adding extra ions to neutralize charge on protein
- adding ions
- Adding Misc. Potentials (e.g. spherical/repulsive restraints/constraints )
- Adjusting Density of waterbox used by solvate
- ADP again
- affecting the atom velocities
- Alchemical FEP calculations in NAMD
- Alchemical FEP NAMD tutorial - problems with reproducing the results
- Alchemical Free Energy Perturbation
- Alchemical Free Energy Perturbation Simulation
- alchemical transformation
- alchemify FEP
- aligning ligands
- Aligning structures
- all atom simulations with explicit water molecules and langevin thermostat
- all atom simulations with explicit water molecules and langevinthermostat
- All or Nothing at All??
- Altix Performance Tuning
- Altix performances
- Amber and SHAKE algorimth
- AMBER FF and pmf
- AMBER ff system has too high velocities in NAMD
- Amber on with H-bond
- Amber Parameter in NAMD
- AMBER parameters and SMD
- amber parameters for congo red
- Amber PARM Input File Example?
- Amber94 files in CHARMM format
- AMD64 or PIV Prescott ...
- amidated C-terminus (NH2) with OPLS force field
- Ammasso interconnect performance, LDB question
- an aptamer and a lot of stupid problems
- Analysis of NAMD output with CHARMM
- Angle 2, Where is the problem [IMPORTANT]
- Angle CO2 Problem
- ANGLE PARAMETERS (It works now)
- Angles and dihedral generation
- ANN: MDAnalysis 0.3 python library
- ANN: MDAnalysis python library
- Announcement: QM/MM Workshop
- Another question about MD simulation of a domain.
- Another question on Diffusion
- Any flag values returned when executing "minimize" and "run"?
- any script to build membrane+protein+solvent?
- any SD minimization in NAMD?
- Anyone have catdcd-4.0 for BlueGene?
- Anyone having problems under Solaris 7?
- ApoB structure
- Appending to the existing dcd file after restart
- apply force along an internally defined direction
- apply periodic boundary condition in one direction
- Applying conformational constraints during simulation
- applying experimental constraints to a MD simulation
- Applying SMD to a domain of protein
- Applying weak harmonic force between two proteins
- April promo on watches
- aquaporin question
- area of a hydrophobic patch
- area per lipid for a protein embedded membrane system
- Area per lipid.
- Argon solvent
- aromatic-aromatic interaction
- Assign the ligand force field parameters
- assigning atom type for parameterization
- Asymmetric water molecule found???
- Atom distance & ptraj
- atom distances
- atom name based paremeters
- Atom number limitations?
- atom numbers limitation
- Atom Positions during simulation
- atom restraints
- atom specification in smd/tclforces for amber topology/parameter based systems
- Atom type explaination for NAMD
- atom type HZ4 not found
- Atomic partial charge
- atomlist command in matdcd
- Atoms mooving too fast ... still the problem
- atoms moving fast
- Atoms moving too fast
- Atoms moving too fast error
- ATP fix (fwd)
- ATP in the Topology file
- ATP molecule
- ATP nucleotides using NAMD
- ATP PDB file
- attractive harmonic potential between 2 molecules
- autocorrelation analysis in timeseries
- autocorrelation function !
- Autogene angles dihed / patch / psfgen problem
- AutoIMD
- autoimd on windows
- autoionize & namd2
- autoionize and psfgen, which one first?
- Autoionize error: spontaneously quits
- Autoionize plugin problem
- autoionize plugin..
- autoionize script
- Autoionize: net charge NOT equal to zero
- Autopsf
- Average energy in NAMD
- Avoiding alpha-helix distortions
- Avoiding Rotation and translation of protein
- Avoiding self-interaction with PME.
- bad exclusion count
- Bad global dihedral count.
- Bad global exclusion count
- bad global exclusion count error
- bad global exclusion count in LES
- Bad global exclusion count.
- balck box: what is the coupling constant when using langenvinFile?
- barostats in NAMD
- basic pdb file run with namd and vmd
- Basic question about steered moledular dynamic(SMD) simulation
- Basic question.
- basic: combining two pdb files?
- benchmarking mistake?
- benchmarking of NAMD: sustained performance (TF)
- Benzamidine parameters
- benzene in NAMD
- Berendsen or Langevin Temp control?
- Berendsen pressure control problem
- Besides PSFGEN, (Thank you)
- Besides PSFGEN, are there any other good ways of generating .psf file
- best choice of linux cluster to run NAMD
- Best NAMD version for Rocks 4.3 IBM xseries 3665
- beta-peptides ...
- big systems using namd on 700 cpus
- BigDCD
- bilayer thickness in simulation of POPC membranes
- Binary conversions
- Binary for MacOSX-i686
- binary install question
- binary restraint reference coordinates?
- binary troubles
- binary.coor to ascII.coor
- binaryoutput option doesn't work for dcd file
- binding constant
- Binding Energies for a Peptide-RNA System
- binding energy
- Binding energy analysis
- Binding Free Energy
- binding free energy , binding constant
- Binding free energy by LIE
- Binding free energy of a protein complex
- Bio-Image summer school in Paris this year
- biotin charmm topology/parameters
- Bizarre atom behavior
- Boiling temperature of water.
- BOND CP2 - CT2 IN PARAMETER FILES
