NAMD-L: By Subject
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About this archive
Starting: Fri Jan 02 2004 - 12:06:46 CST
Ending: Wed Dec 28 2005 - 17:21:37 CST
- "Constrain failure" in NAMD
- "GRADIENT TOLERANCE: nan", Why?
- "Hands-On" Workshop on Computational Biophysics
- "make" Linux-amd64-g++ error
- "Segmentation violation" on running namd2.6b1
- # of processors
- (no subject)
- ***** SPAM POSSIBLE ***** Warning: Not all atoms have unique coordinates.
- ,log and .out files with namd running on mac os x (panther)
- 1 D Periodic Boundary
- 1-4 interactions scaling
- 1QSU
- 2.6b1 source missing file
- 32 vs. 64 bits
- 4th Annual Workshop on Charm++ and its Applications 2005
- 64 nodes behaviour
- <no subject>
- > 10000 ato
- > 10000 atoms
- [Fwd: counterion software]
- [Fwd: total energy stuck between two levels]
- [Periodic Boundary]: from charmm to namd
- _alloca undefined symbol (OS X/XL compiler)
- A confused question on amber param and in charmm form~
- a different bug alert
- A question about MD simulation of peptide.
- A question about RMSD calculation
- A question on minimization
- A question on psfgen
- A question regarding generate pdb and psf file
- A strange thing about psfgen~
- a target molecule in a water box.
- A tool to set up alchemical FEP transformations
- abf
- ABF for conformational analysis
- ABF Simulation
- ABF.TCl file ???
- about *.psf
- About ADP
- About calculating RMSD with rmsd.tcl
- About charm++/namd on AMD64 cluster
- about delta-G in PMF calculation
- about ExcludeFromPressure
- about guesscoord
- About ions Representation in NAMD
- about MCTI output
- about membrane protein
- About PDB file with fixed atom flags.
- about pmf
- About Potential Addition in NAMD
- about protonation of HIS in membrane protein
- about psf file
- About Restart
- about rigid bonds
- About RMSD calculation.
- about symmetry operations
- About the command "loadtotalforces"
- About the potantial of IONS
- About the potential of NAMD
- About the Source code.
- about this bug alert
- ABSOLUTE IMPRECISION and RELATIVE IMPRECISION IN TABLE FORCE
- Accessing beta / occupancy values from NAMD tcl
- add ions
- 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 ions
- Adding Misc. Potentials (e.g. spherical/repulsive restraints/constraints )
- Adjusting Density of waterbox used by solvate
- Alchemical FEP calculations in NAMD
- alchemical free energy perturbation
- alchemify FEP
- All or Nothing at All??
- Amber and SHAKE algorimth
- AMBER FF and pmf
- AMBER ff system has too high velocities in NAMD
- Amber on with H-bond
- AMBER parameters and SMD
- Amber94 files in CHARMM format
- AMD64 or PIV Prescott ...
- Ammasso interconnect performance, LDB question
- Analysis of NAMD output with CHARMM
- ANGLE PARAMETERS (It works now)
- Another question about MD simulation of a domain.
- any script to build membrane+protein+solvent?
- Anyone having problems under Solaris 7?
- aquaporin question
- area of a hydrophobic patch
- Argon solvent
- Assign the ligand force field parameters
- Atom number limitations?
- atom numbers limitation
- Atom Positions during simulation
- atom specification in smd/tclforces for amber topology/parameter based systems
- Atom type explaination for NAMD
- Atoms moving too fast
- ATP in the Topology file
- ATP nucleotides using NAMD
- ATP PDB file
- autocorrelation analysis in timeseries
- autoimd on windows
- autoionize & namd2
- autoionize and psfgen, which one first?
- Autoionize plugin problem
- autoionize script
- Autoionize: net charge NOT equal to zero
- Avoiding Rotation and translation of protein
- Bad global exclusion count
- Bad global exclusion count.
- basic: combining two pdb files?
- benchmarking mistake?
- benzene in NAMD
- Berendsen or Langevin Temp control?
- Besides PSFGEN, (Thank you)
- Besides PSFGEN, are there any other good ways of generating .psf file
- best choice of linux cluster to run NAMD
- beta-peptides ...
- binary restraint reference coordinates?
- 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 of a protein complex
- Bio-Image summer school in Paris this year
- BOND CP2 - CT2 IN PARAMETER FILES
- bonding to image
- Box Dimension
- Box size
- box size changes under anisotropic pressure coupling
- Bringing Up To Temp
- Bromine
- Bug alert!!!
- BUG ALERT: Bad global exclusion count!
- BUG ALERT: Hydrogen group error caught in rattle1
- BUG ALERT: Mother atom with hydrogenGroupSize of 0!
- BUG ALERT: Stray PME grid charges detected.
- Bug in Pair force interaction calculation was fixed?
- bug report and stray pme
- build charm on ia-64 linux
- building charm++ on macosX
- Building NAMD 2.6b1 on IBM Power5
- Building NAMD with Portland's C++ Comipler
- c-shell into NAMD configuration file
- CA CL CA angle?
- Ca trace only
- Ca++ topology¶m files
- calculate energy with water excluded
- calculate enthalpy of binding
- Calculate Potential Energy
- calculate the binding energy or binding free energy?
- Calculating forces
- Calculating Free Energy Change
- Calculating parameters.
- Calculation of velocities
- Can extending MIN solve the problem of "Constraint failure in RATTLE algorithm"
- Can I miminimize some atoms in system
- can i restrain the center of molecule in aqueous solution?
- Can NAMD control pressure gradually increase?
- Can NAMD deal with solid-state system?
- Can we fix the position of two atoms while minimization?
- CAN'T FIND BOND PARAMETERS FOR BOND (error)
- CAN'T FIND BOND PARAMETERS FOR BOND FE - S
- capping by psfgen
- capping using Amber FF
- Catdcd
- catdcd and dcdunitcell
- catdcd-generated files and CHARMM
- CCS ERROR during simulation
- Cell Basis Vector.
- Cell Basis Vectors
- cellBasisVector x,y,z values
- cellBasisVectors and xsc files
- cellOrigin
- center of mass motion: problems
- cff91 force field in namd
- cff91 force field in namd + A Question
- Chamrun/NAMD processes and PBS cluster
- changing default directory in VMD?
- changing file
- Changing SMD parameters
- changuing dihedral angle slowly
- changuing dihedral angle slowly (complete message)
- charamrun / Rocks distribution problem
- charm++ 5.9 build fails, NAMD 2.6b1 make fails
- charm++ 5.9 megatest failure too
- charm++ compile problem on x86_64
- charm++ mpi-linux compilation errors
- charm++ MPICH and Myrinet
- Charm++ nodelist commands
- Charm++ Problem
- Charm++ problem on EM64T/Myrinet cluster
- charm++ with gm
- CHARM/NAMD network problems on amd64 Clustermatic
- CHARMM
- Charmm 1,4 Interactions - Scaling Question
- charmm and dihedral multiplicity
- CHARMM compatible Methotrexate params
- charmm parameters for PEG
- charmm paramter
- charmm restart file
- Charmm++5.9 build on Mac OS X by IB xlc compiler
- charmm->gromacs->charmm force field conversion
- charmm27
- charmm27 fatal error
- Charmm27 Xplor format
- charmrun vs. miprun and nature of parallelism
- checking for correct construction of dihedrals, etc.
- Checkpoint on IRIX of namd 2.5 job not MPI enabled
- Chloroform Solvent Box
- Class I vs Class II force fields
- clustering
- clustering - fault tolerant NAMD
- clustering macs
- clustermatic 4 and 5 Namd/charm
- Clustermatic 4.0
- Clustermatic 4: Charmrun> error 1 attaching to node:
- clustermatic nodelist file
- Clustermatic PCI IDs
- Clustermatic with SCSI
- CMAP in CHARMM force field
- CMAP in VMD error
- coarse grained force field
- coarse grained model
- CoM motion not removed
- COM position
- COM velocity
- Combine pdb and psf files
- command to run MPI and ABF
- Common Problem!: Periodic cell has become too small for original patch grid!
- communication with NAMD?
- Compilation of Charm++ on Linux opteron cluster with MPICH-GM installed
- Compilation of NAMD on 64-bit NUMA
- Compilation of NAMD on 64-bit NUMA with icc
- Compilation of NAMD on opteron cluster with myrinet
- Compilation on an Opteron Server SuSE Linux Enterprise System Version 8
- Compilation on Opteron
- compile "mpi" charm++ on amd64
- compiled namd on clustermatic fails !
- compiler flags.
- Compiling
- Compiling charm on a opteron cluster
- Compiling charm++-5.9: Problems with g++
- compiling linux scyld mpi 64bit
- compiling NAMD
- Compiling NAMD from SRC: Tungsten@NCSA
- compiling NAMD on a redhat-pentium-dell workstation
- compiling namd on amd opteron arch : TCL problems (fwd)
- compiling Namd on amd64
- Compiling NAMD on IA64 cluter
- Compiling NAMD on Linux cluster
- compiling NAMD on OSC P4 cluster
- Compiling NAMD on Tungsten.ncsa
- Compiling NAMD with mpicc myrinet
- compiling NAMD: plugins
- Compiling on G5 using xlC
- Compiling on Linux-PPC970-Myrinet-MPI-xlC
- Compiling the NAMD on HPUX-ia64 system Error!
- Complementary programs for NAMD
- Complie NAMD on Suse Linux
- Compliling NAMD in RedHat9
- computing resource
- concatenating two DCD files
- concatenating two or more dcd files
- Condition for stopping MD sim. with NAMD
- conditional statements in conf files
- config files
- conformational alignment
- constant angle NPT simulation
- Constant pressure contril
- constant velocity smd with distance restraints
- constrain or fix the system only in Z direction
- constraining center of mass-constrained MD
- constraint constant in equilibration
- Constraint failure
- Constraint failure in RATTLE again
- Constraint failure in RATTLE algorithm
- constraintScaling parameter
- construct a protein surrounded by membrane
- convert DCD files to GROMACS .XTC format
- convert namd structure/coordinate files to gromacs topology file
- convert_from_namd_to_amber
- Converting Gromacs OPLS parameters to Charmm format
- Converting Gromacs parameters to Charmm format
- Converting PSF TYPES: from XPLOr to CHARMM
- counterion software
- counterions
- Counterions: how to decide how many to put it?
- covalent bonds across periodic boundaries
- CP3-NH3 error
- Crash during free energy calculation (MCTI)
- crash in FFT optimizing...
- creating a pdb file based on sequence and psi phi omega values only
- creating Charmm psf from Xplor format
- Creating Parmtop files for NAMD
- cross products
- D-amino acids
- dcd files generated with catdcd
- dcd format
- Dealing with hyperthreading
- define abf1 and abf2 for CM of water and CM of molecule
- density calculation
- developing parameters for charmm
- dielectric constant
- difference between two kinds of dimers
- Different electrostatic and Van der Waals cutoff
- different result from different cpu
- different result when I run the same *.conf file many times.
- Different solvents
- difficulties using SMD on atoms in large systems
- Dihedral and Improper, Nonbonded.
- DIHEDral drift ?
- DIHEDral drift [2] ?
- Dihedral restraint
- Dihedral restraint : question closed
- dimer minimisation and psfgen problem
- Direction of SMD force
- Direction of the force in Pair interactions
- Discrepency in cell volume? Cell origin can move in NPT?
- distance constraint
- distance constraints in NAMD
- distance dependant dielectric constant
- distance restraints during a dynamic
- dmpc membrane
- Does anybody have gromacs topology example, which works OK using NAMD??
- Does NAMD calculate the potential energy of FIXED ATOMS?
- Dose restart frequently affect the results?
- DOWSER
- DPPC
- dramatical standard deviation in the pressure profile
- Duplicate lines in the output file !
- duplicated key CA in psfgen
- Dynamically resizing waterbox
- Edge Water in PBC
- Effect of FullDirect electrostatics
- eigenvector projections
- ELECT energy
- Electric Field
- electron density calculations of lipid bilayers
- electron density profiles (EDP)
- Electrostatics energy calculation
- electrostatics under spherical harmonic conditions
- energy
- Energy Determination
- Energy for part of system
- energy minimization
- Energy minimization at NAMD
- Energy Order of Magnitude
- Energy Problem (Order of Magnitude)
- energy values
- ensemble
- entropy calculations
- equilibrated the system
- equilibration of protein in water box
- errno = 2
- error
- error codes in charmrun/namd?
- error in config file
- Error in running tutorial files
- Error in temperature calculation
- Error in when using charmrun
- error message
- Error on Solaris
- Error opening XSC output file...Invalid argument
- error parsing config file
- error running namd
- Error when running NAMD at SDSC
- ERROR: Constraint failure in RATTLE algorithm for atom 127!
- ERROR: Constraint failure in RATTLE algorithm for atom 598!
- ERROR: Margin is too small (BUG?)
- error: Number of atoms in fixed atoms PDB doesn't match coordinate PDB
- error: UNABLE TO FIND ANGLE PARAMETERS FOR C NH1 C
- errors building charm on ia64
- Errors compiling NAMD 2.5
- Errors: Periodic cell became too small for original patch grid & Setting parameter binaryoutput from script failed!
- essential dynamics analysis
- estradiol
- Euro QSAR 2004
- example scripts
- extra points in NAMD
- Extra terms in the expression for potential energy
- extracting time from DCDs
- Failed to set coordinate for atom errors!
- fatal error
- Fatal error on PE 0> FATAL ERROR: DIHEDRALS INDEX 150255520
- fatal error running namd
- Fatal error:
- FATAL ERROR: Asymmetric water molecule ?
- FATAL ERROR: Asymmetric water molecule??
- FATAL ERROR: child atom 39 bonded only to child H atoms
- FATAL ERROR: Patch needed for tuple is missing.
- FATAL ERROR: Stale NFS file handle
- FATAL ERROR: Tried to find atom type on node other than node 0
- FATAL ERROR: UNABLE TO FIND ANGLE PARAMETERS FOR CN7 CN7 CN7
- FATAL ERROR: unknown floating-point error, errno = 4
- Fatal Socket error
- Fatal Socket error: code 93523-Error in accept
- Fe2+ parameters?
- Fedora Core 4 problems (?) ...
- Fedora Core 4 problems [2] ...
- Feedback on "alchemify" tool
- fep
- FEP - one long simulation vs many short ones
- FEP alchemical
- FEP and restraints
- FEP and solvent
- FEP and TI
- FEP calculations: defining hybrid residues
- FEP charge perturbation
- FEP error: Rattle atom constriant
- fep file
- FEP output in NAMD
- FEP setup
- FEP....
- Ferric heme
- Finished install
- firsttimestep
- FIRSTTIMESTEP in config file
- firsttimestep: simple question
- fix backbone atom
- Fix distance
- fix or Harmonic constraint ?
- fixed atoms
- Fixed atoms and dcd file with DCDunitCell on
- fixed particles
- Fixed restraint
- Fixing atoms during simulation
- Fixing position of COM
- FK506 ligand topology file(1FKF)
- flexible cell
- flexible cell for MD simulations
- flipDCD and Unit Cell information?
- Fluorophors ?
- for help from all!
- For help with .log file.
- force calculation
- Force Calculation in NAMD
- Force constant of harmonic restraint
- force constraints
- force shifted cutoff
- Free Energy of Conformational Change Calculations Error: "Problem parsing input parameters Error: Invalid AtomID"
- free energy pertubation,binding energy and constant
- freeEnergy of conformational change of a test molecule
- Fwd: All or Nothing at All??
- Fwd: missing atom prob
- Fwd: Parameter file.
- Fwd: PSFgen error
- Fwd: vmd-l: MOE discussion
- G5 cluster
- G5 clusters
- gcc and G5 Xserves
- gcc4
- GdHCl parameters
- General and specific atom types in NAMD?
- General question about NAMD
- Generate psf file of DMPC membrane
- Generate PSF structure
- Generating a lot of segments in proper order and selection around a center of mass
- Generating novel structure
- generating psf files (and more!)
- Generating psf files for non-proteins
- generating PSF files using CHARMM for FEP calculations
- Generating psf for a drug, trimethoprim
- generating psf for RNA using psfgen
- Generating simulation with large conformational changes
- Generating topology file
- geometric mean
- Getting forces: segmentation violation or illegal instruction
- glucose CHARMM force field
- gradient nan
- Gradient Tolerance
- Gradient tolerance--total or per atom?
- Gramicidin
- Gromacs force field paramets: Syntax error in ATOMS
- Gromacs parameters in NAMD
- GROMACS to CHARMM
- gromacs/gromos96 force field
- H-H bond in solvate
- H-H bond in TIP3 water
- hanging at startup phase
- hanging at startup phase 0
- Haptic Device
- hard wall
- harmonic restraint
- Harmonic restraints for moving residue positions??
- Has NAMD been ported to Itanium2 + Linux?
- hbonds output!!!
- Heat Capacity & Relaxation Functions
- help generating psf files
- Help with psf and par for small molecules
- Help with SMD
- Help! There is no angle or dihedral definitions for patches in .psf!
- Help, MD run errors
- HEM residue in NAMD
- Heme A topology?
- HEME patch
- Hessian
- Heteroatom entries
- Hexagonal cell and PME grid.
- hexagonal unit cell
- Hi
- hi ,everyone.I have a problem about random force
- hi all, I want to know how to turn the debug mode on of the namd
- Hi, call NAMD from C
- Hi,how can I generate a psf file with a pdb file contain some special amino acid like TYS
- HIERARCHY OF INTERACTIONS"
- high (or low) pressure readings
- How can I increase the computing rate on the computer cluster
- How can I move an atom by 10nm with a step of 0.1nm
- How do I Heat, then Switch to NPT in the same *.config?
- How do we combine chains in the end
- How do we know the velocity?
- How do you specify which coordinates are to be fixed?
- How does NAMD calculate Electrostatic potential energy (no periodic boundary condition)?
- How I can get the hole program?
- How I can run two simulations one after an other
- how is NAMD output written in parallel mode?
- how many steps do we need do for energy minimization ?
- How MD stopes at a specific distance?
- How to "extract" coordinates from a DCD trajectory file?
- How to append charmm stream file
- how to apply a random force on a atom
- How to atomselect several residues
- how to build AQP1 tetramer
- How to calculate specific heat capacity in NAMD?
- How to change psf file in the half way of VMD simulation?
- How to chech the harmonic constraint work normally~
- How to Compile NAMD on HPUX-ia64 system~
- How to conservate energy during NVE simulations???
- how to constrains the smd atom on a line when do my smd simulation??
- How to create a substrate parameter file ?
- How to decide the protonation of some residues??
- how to disable NTER and CTER patches?
- How to do pH simulation on NAMD?
- how to fix some atoms?
- how to fix the atoms of backbone ?
- how to generate your own pdb file
- how to get "the rms force and maximum force" of energy minimization ?
- how to get hydrogen-bond energy?
- How to have neutral terminal ends
- how to image molecules back into a PBC box
- How to make a negatively charged surface
- How to make a surface
- How to move COM during minimization?
- How to patch segments of aminoacids
- how to read amino acid such as 27, 27A,27B,27C in pdb file?
- How to read charmm binary trajectory file using home-made C/C++ code
- how to remove all hydrogen atoms from PDB file?
- how to restart/continue NAMD run
- How to run for periodic boundary Conditions?
- How to run namd on NCSA Tungsten
- How to set a molecule to be rigid in NAMD?
- How to treat the terminal residue psfgen in NAMD~
- How to use AMBER force field in NAMD?
- how to use gromacs force field in NAMD?
- how to use restrain command in configuration file in NAMD.
- How to use restrin command in NAMD configuration file
- how to use the dual-processor machines
- Hybond calulator and display
- hydrogen bonds during MD
- hydrogen bonds in NAMD
- Hydrogen cut off distance
- hydrogens collapsing
- Hydroxyprolin force field.
- HYP files
- HYP parameters
- HYP residue and unknown residue type NH2
- IA64 and MPICH and mpiexec runtime shmem errors
- IC Removal and Problem
- icc compilation problem
- Illegal instruction signal at startup. (with net-rs6k smp)
- implementing angle dependent non-bonded interaction?
- implicit solvent
- implicit solvent model
- Implicit water dielectric constant.
- improving parallel on mac cluster
- incompatibility between VMD & NAMD for reading Amber crd files
- inconsistencies with amber force fields due to scnb and 1-4scalin g
- Incorrect periodic box imaging with AMBER parameters
- increase in energy over time
- Increasing temp during MD
- Infiniband and PME gridsize
- infinite DNA
- Influence of PME grid size and cell basis vectors over simulation result
- Info about forces on atoms
- initial temp of simulation
- initial translation of the system
- inorganic surface peptide simulation
- Installing NAMD
- Installing NAMD on beowulf cluster, 64 bit, opteron, 4 processors.
- installing NAMD on opteron cluster with MPI
- installing on beowulf cluster
- INTEL 8.0 optimization flags
- Intel C/C++ compiler Version 8 for compiling NAMD on IA64
- Interaction between metal and metal-water.
- interaction energy
- Interaction energy between fixed atoms
- Interaction energy for fixed atoms
- interactions in flexible cel
- interactions in flexible cell
- Interactive Simulations, ligand size limits....
- interface with external program
- IO error when running NAMD on new cluster
- ion concentration
- Is it necessary to neutralize the system with NAMD program?
- Is there a method to choose what is saved in DCD files
- isotropic pressure tensor
- Issues with SMD
- It appears that the Claim that NAMD works with gromacs is false
- It is posible to allow Bond and angle degrees of freedom in tip3 water??
- it is posible to do NVE simulations in NAMD???
- Job is terminated in the middle
- Kinetic energy
- Kinetic Energy difference using restart binaries
- langevin coupling coefficient
- Langevin dynamics
- Langevin Dynamics again
- langevin vs coupling to a heat bath
- langevin with waterbox ?
- Large Box Sizes and Total Energies Observed in NAMD 2.6b1 Binaries of AIX-POWER-MPI and Origin2000-MPI
- large increase in pressure after minimization
- large vanderwalls energy during minimization
- last call for early registrations for "Horizons2005"
- Layers
- LDB question
- learning how to do a Cys palmitoyl patch
- libimf.so error when compiling charm++
- libimf.so problems
- ligands in VMD
- limit on the number of residues in each segment
- Link Ammasso MPI with NAMD
- linux cluster trouble
- Linux-MPI binary of NAMD 2.6b1
- Lipid membrane simulation by NAMD
- Lithium
- Load balance strategy
- loadtotalforces: 1000+ pN per atom!
- Locally Enhanced Sampling
- log file
- loodking or topology file for zinc finger
- mac clustering
- make namd2 problem
- Making PSF file
- Manipulating structure
- margin errors
- Margin violation
- MD stops when COM or atom reaches a distance
- MDenergy error
- mean square displacemente and diffusion of water at T=298 K
- Megatest fails on Linux cluster
- Membrane configuration file
- membrane files
- membrane protein md protocol
- merge trajectory from NAMD
- Metal Ion and Protein binding
- Methane residue file
- Milestoning in NAMD
- mimization warnings - bad global exclusion count
- Minimization after a MD simulation
- minimization problem
- minimization problem - "Bad global exclusion count, possible error!"
- minimization problem - "Bad global exclusion count,possible error!"
- Minimization questions...
- minimization scripts
- Minimization with CHARMM
- Minimization with NAMD
- Minimizing and Equilibrating
- minimum imgae convention
- missing atoms warnings for psfgen
- Missing coordinates and psfgen
- MM/PBSA
- mmtools
- Modeling a polymer
- modeling sucrose
- Modified DNA bases PDB files
- modifying cut off
- Molecular Dynamics or Langevin Dynamics
- molecules distorted
- Momenta output format
- moments of inertia, principal axes
- more Heme troubles
- More NAMD/gm2 problems
- more than 99999 atoms in PDB files
- Mother atom with hydrogenGroupSize of 0
- Move molecule
- mpi opteron myrinet
- mpi problems on opteron
- multiple automated calls to NAMD
- Multiple dihedral multiplicity
- Multiple Harmonic Constraints
- multiple jobs on a cluster
- multiple MD simulations
- munch: The input file main.o is not valid in the current object mode
- Myrinet and MPI
- Myrinet and MPI question
- Myrinet NAMD
- Myrinet vs. Infiniband
- Na ions got into the catalytic site during Production Run
- NADP hydrogen zero
- NADP problem
- NADP topology
- NAMD "freezes" up
- NAMD "freezes" up (further clarification)
- NAMD & Gromacs FF
- NAMD 2.5 crashes unpredictably on a 8 way SMP (Linux x86)
- NAMD 2.6 in IBM SP
- namd 2.6b1
- NAMD 2.6b1 error writing DCD file on Cray XT3
- namd 2.6b1 job crash error
- NAMD 2.6b1 Released
- NAMD 2.6b1 Skipped Writing Velocity Restart File
- namd 6-1- abf
- NAMD and dual core Opterons, thoughts?
- namd and fftw
- NAMD and Gromac OPLS parameters
- namd and node freeze
- namd and Tcl 8.3.5
- NAMD and Vega?
- NAMD at Data Star SDSC
- NAMD attempting to read FFTW
- NAMD automation
- NAMD C++ API
- NAMD cluster run
- namd cluster run, connection refused
- NAMD crashes with LES option ON
- NAMD distribute
- NAMD Energy Plugin
- NAMD for Opteron?
- NAMD for Xeon clusters
- namd hangs
- Namd hangs on Bproc cluster
- NAMD interaction with VMD
- NAMD job abnormally killed with PBS
- NAMD linking problem
- namd linux source or binary
- NAMD Myrinet issue - Strange behavior
- NAMD node freeze
- namd on Altix
- NAMD on dual opterons
- NAMD on fedora 3 core?
- NAMD on HP with Itanium2 Processors
- NAMD on HP-IA64 Linux
- NAMD on IBM cluster AIX-RS6000
- NAMD on IBM pSeries (690, 655)
- NAMD on Intel XEON EM64T
- NAMD on itanium?
- namd on lemieux
- namd on linux cluster
- NAMD on Linux cluster with Myrinet
- Namd on Mac os X
- NAMD on myrinet
- NAMD on new P4
- NAMD on OpenMosix.
- NAMD on OSX built with XLC?
- NAMD on p690 IBM cluster
- namd on PPC, linux
- NAMD on PSC
- NAMD on SUN
- NAMD on the TeraGrid
- NAMD on Win64
- NAMD on Xeon EM64T
- NAMD parser
- namd performance on altix machines
- NAMD prog. guide
- NAMD programming guide
- NAMD recognizes only one MPI process
- Namd RedHat9 compilation problem
- NAMD restarts binary files
- NAMD running only at 40-50% CPU capacity
- NAMD running problem
- NAMD simulation: HEME
- NAMD Source
- NAMD support for Myranet GM2 drivers
- NAMD time step: AKMA?
- NAMD with Amber
- NAMD with HPUX/IA64.
- Namd with intel compilers.
- namd-L: tcl script for calculate RMS of MD calculation
- NAMD-MPI compilation on P4 cluster
- NAMD/CHARM source installation option
- NAMD/iAPBS
- namd2 compile linux-i686-mpi
- namd2 mpi error
- NAMD2.5 and the TeraGrid
- namd2.5 on linux-cluster
- namd2.5 on myrinet cluster
- NAMD2.6b1 (&2.5) binaries on Scyld (missing libbproc.so.2 lib?)
- Namd2.6b1 FATAL ERROR: Memory allocation failed on AIX53 IBM-SP4
- namd2.6b1 hang on IBM p-690
- NAMD2.6b1 on an OSX cluster
- namd: advice
- NAMD: error messages
- NAMD: Force Fields
- NAMD: HEM residue
- NAMD_2.6b1 shared lib problem on amd64 clustermatic using intel compilers
- NAMD_utilities
- NamdCompile Problem
- namddat not working
- namddat: Command not found
- namdplot
- namdplot error
- namdplot not working
- namdplot, graph is empty
- namdplot, grpah is empty
- namdplot: command not found
- namdstats
- NAN GRADIENT TOLERANCE - & - RESTARTING CONJUGATE GRADIENT ALGORITHM
- NANMD errors: PME, qsub
- Nanotube psf file.
- Nanotube simulation in water problem
- Nanotube Simulations
- NBFix command to apply Lorentz-Berthelot mixing rules
- Need of an ASCII-PHI converter, any help is appreciated to use wat2ions from Delphi output
- Need to add Hydrogens to over 300 distinct PDB's
- new approach to counter FEP end-point VDW clashes
- New BioCoRE server released
- New cluster configuration?
- new problem
- NMAD job abnormally killed with PBS
- Node 0 could not initialize network!
- Node list
- NOE constraints with NAMD
- non-repeatability NAMD simulations
- Not all atoms have unique coordinates - revisited
- Not getting good speed up
- NPT and FIXED atoms
- NPT calculations in NAMD
- NPT ensemble restart, put in new basis vectors?
- Number of Steps
- numerical inaccuracy upon restart
- Obtain message from MD
- octahedral period BCs
- Only part of the protein is moving in MD simulation
- opinions on queueing system choices?
- opteron 64bit installation
- optimisation for dual CPU sytem
- Order of improper dihedrals
- output files always go to same node
- Output files creation problem in MPI.
- output in tcl
- Output only protein .dcd
- output to multiple files
- Packaging 100 cations and anions in a box
- Pair interaction calculation for large number different pairs
- pair interaction calculations
- Pair interaction calculations in precompiled NAMD
- Pair interaction energies: TCL error
- Pair interaction energy
- pair interaction forces
- Pair Interaction options
- Pair interaction output.
- Pair interaction, PBC included?
- pair interactions in NPT
- pair-interaction energy
- pair.pdb and cutoff for pairInteraction
- pairInteraction energies?
- pairlist distance
- palindromic error reading in a restart file.
- Paper on Classical treatment for calculating pKas
- par_all27_prot_lipid.inp
- Parallelization of a code from TCB Summer School 2003
- parameter and topology for 4-MI
- Parameter file again.
- Parameter File Problem
- Parameter file.
- Parameter files for Nanotube Simulation
- Parameters and topologies for aa at different protonation states
- Parameters for iodine atoms
- parameters for NAD,NAG,NAP
- parameters for NVT ensemble
- Partial charges for fluorescein/topology file
- Patch
- patch failed
- patch PYRT and extending DNA
- path problems
- pause simulation
- PBCwrap: wrapping DCD files
- PC-DL Deluxe, Dual Xeon
- PDB files for carbon nanotubes
- Penetration of water
- peptid bond omega, problems with settings?
- peptide out of the water-box
- peptide simulation
- performance differences on 2.4 vs. 2.6 Linux kernels
- peridic boundary condition
- Periodic Boundary Condition
- Periodic boundary conditions
- Periodic Boundary Conditions and Wrap
- Periodic cel too small
- periodic cell has become too small
- Periodic cell has become too small for original patch grid
- Periodic cell size
- Periodic cell too small
- phase equilibria using NAMD
- phosphoserine
- pka calculations and their use in simulations
- plugins.tar.gz & charm_src.tar.gz !!!
- PME ERROR
- PME grid sizes
- PME off
- PMEGridSize
- PMEgrindsize for hexagon
- pmf
- PMF Calculation
- PMF calculation using fixed restraints
- pmf error
- PMF force restraint question
- Poorly guessed coordinates
- POPC or POPE?
- Position of the Virtual atom
- Potential energies in TCL interface
- Potential Terms
- preparing a dimeric protein for NAMD
- preparing a dimeric protein for NAMD (Thank you)
- pressure
- pressure control in config file
- pressure profile
- Pressure Profile Simulation
- Pressure tensor and periodic boundary condition
- Pressure_control
- previous question about multiplicity
- prmtop reading error
- problem about equilibration
- Problem in restarting simulation
- problem running namd
- Problem using Gromacs topology file
- Problem using the GROMACS force field !
- problem using visual_mdenergy: program has trouble reading the dat file
- problem when do equilibration
- problem when heating the system
- problem while running NAMD
- Problem with compiling NAMD on Suse 9.3
- Problem with mdenergy
- Problem with NAMD on Opteron cluster
- problem with PSFGEN
- problem with PSFGEN: the O3A atom cannot be recognized
- Problem with PSFGEN?
- problem with running namd on Linux cluster
- Problem with solvate and PSF files in CHARMM format
- Problem with Tcl & psfgen
- problem with the NAMD CPU time consumption on a batch queueing system
- problem:psfgen- not unique coordinates
- Problems compiling Charm++ for Myrinet
- Problems compiling NAMD on linux/clustermatic 5
- problems NAMD_2.6 (fwd)
- problems on Fedora Core 3
- Problems opening the Extended Trajectory File
- problems with autoionize total charge and minimization
- problems with namdplot fixed by using new plotting program
- Problems with the nodelist file !
- Problems witn parameter files!
- Processor load
- protein interact with its image
- Protein moving out of PBC water box
- protein/DNA complexes
- Protonated aspartic acid
- Protonated GLU/ASP in PSF generation
- Protonation state of HIS
- PSC WORKSHOP: COMPUTATIONAL BIOPHYSICS WORKSHOP
- PSF file ATP
- psf file for zeolite-water system
- PSF file format
- PSF file generation
- psf question
- PSFGEN
- psfgen : wrong guess for leucine hydrogen
- psfgen and extending 5' end of DNA
- psfgen and poorly guessed coordinates
- psfgen error "Missing atom for conformation definition"
- psfgen for DNA
- psfgen issue
- psfgen non-bonded atom pairs
- psfgen patches
- psfgen problem
- PSFGEN problems in nanotube tutorial
- psfgen question
- psfgen trouble with heme
- Psfgen within NAMD
- psfgen/auto none
- psfgen: failed on segment
- Pt LJ Parameters
- ptraj
- pulling plus restraint
- Qestions about NPT simulations.
- qsub
- query on memory usuage
- question (fwd)
- question about autogen in topology file
- Question about Constraint failure in RATTLE algorithm for atom
- Question about cutoff distance
- Question about external forces
- Question about Generating DCD files with only specified atoms
- Question about Gradient Tolerance during minimization
- Question about load balancing
- question about nonnbonded parameters
- Question about pair interaction feature
- question about par_all27_prot_lipid.inp
- question about patch
- question about running equilibration in NAMD
- question about using Amber force field in namd
- question on a chared system MD simulation
- question on autocorrelation function and temperature controlling
- question on Berendsen's temperature coupling method
- Question on finding suitable force field for MD simulations
- question on force autocorrelation function
- Question on harmonic constraints
- question on Lithium force field
- question on pair interaction energy and force
- question on PMF output
- question on potential energy for individual atoms
- question on running NAMD2 using Amber files
- question on running NAMD2 using Amber files (fwd)
- question on self-diffusion constant of TIP3P water
- question on tcl script for rmsd calculation
- question on the coordinates of hydrogen atoms
- question on the parallel job on NCSA Xeon cluster
- question on the wrapping algorithm in NAMD
- question on veldcd
- Question regarding SMD
- Question:about equilibration~
- Question:about harmonic restraint decrease!
- Questions
- questions about "psfgen".
- questions about anisotropic pressure coupling
- questions about applying patches
- questions about running namd on NCSA cluster tungsten
- questions about set cellBasisVector and a ligand ...
- Questions on periodic boundary condition
- Radial Distribution Function
- Random forces in Langevin temperature control -- three questions
- random seed
- RATTLE Alg
- RATTLE and DNA
- rattle errors.
- Re water box and system charge
- Re. van der waals energy
- Reading from DCD file and running MD
- Recalculating energies from DCD file
- recentering protein in the waterbox
- recommendation for 32 CPU cluster: Opteron or ?
- reconstruct PMF
- reconstructing backbone with psfgen
- Regarding SMD atom and forces
- regenerating PSF file
- Regulating density of water
- relating FEP-derived ddG values to experimental IC50
- removing a covalent bond during a simulation
- removing water from DCD
- render format
- replica exchange
- replica-ex NAMD?
- Replica-Exchange MD
- Report on a trajectory incompatibility between NAMD and CHARMM: Unfolding and RDFs
- rescaling of coordinates in PBC simulations
- Reset
- Reset reference position
- resetting restartfreq parameter
- Residence time
- resolved: BUG ALERT: Mother atom with hydrogenGroupSize of 0!
- restart a simulation
- restart files
- restart files after minimization?
- restart problem
- restart simulation
- restart syntax
- Restart using amber force field
- restarting a simulation accurately
- RESTARTING CONJUGATE GRADIENT ALGORITHM
- Restarting problem with Langevin dynamics
- restarting SMD jobs
- Restartname
- restraints
- retinal parameters
- return molecule to its principal axes
- Reverse Free Energy perturbation (FEP)?
- rigid bonds for other atoms
- rigidBond water
- rigidBonds water
- rmsd and simulation
- rmsd calculation
- rmsd problem
- rmsd problem,script and version
- Rotating a structure about an atom
- rotating constraints
- rotating constraints constant
- rotation constraint angular velocity
- rsh on nodes
- run NPT equilibration
- Runnig same config file many times
- Running AIX version of NAMD on IBM cluster
- running multiple minimizations
- Running NAMD 2.6b1 on Linux Networks
- Running NAMD on a multiprocessor computer
- Running namd on Rice Teracluster
- running NAMD on tungsten
- running NAMD2 in parallel
- Running on Alpha cluster
- running on two different machines....
- running VMD from a script?
- running VMD from a script? -- oops, never mind!
- Sample Configuratiion files
- Sampling trajectories
- saving coordinates as a PDB file after minimization in NAMD
- saving forces using loadforces
- saving picture from namdplot
- Scale on Force vs Time plot?
- scaling issue
- scnb scaling factor and compatibility with AMBER force fields
- Script for calculating energy of a water molecule
- Script for MD in a loop?
- scripts for binding free energy calculation using SMD and Jarzynski's equality
- scyld no longer a supported option for building charm++ ?
- seed value in SMD
- segfaults in mm_malloc
- Segmantation fault writing dcd files.
- segmantation violation
- Segment atom number limitation
- segmentation fault on Linux
- Segmentation fault with two processors
- Segmentation fault.
- Segmentation violation
- Segmentation violation in NAMD !
- segmentation violation!!
- selectConstrZ
- Serious Steric Atom Clashes
- set center
- setting configuration file for free energy perturbation
- setting constraints to off in execution script
- Setting target minimization gradient?
- SGE (Grid Engine) on Rocks Cluster
- shake and minimzation, equilibration
- SHAKE or not?
- shape change of water box and peptide move out
- shmget error
- Simulated Annealing Config
- simulated annealing step size
- Simulation terminating due to RATTLE constraint failure
- Simulation with ammonia
- simulations ceased without any hint
- Single point energy calculation
- Size of water box
- SMD
- smd and loadforces
- SMD and minimizations
- SMD atoms not read properly!
- SMD by pulling two groups apart
- SMD force
- SMD force (fwd)
- SMD on a group of atoms: Confusion
- SMD with different pH
- SMD-drifting of center of mass
- SMD-velocity unit
- SMD: Group of atoms COM fixed?
- SMD: many atom pulling
- socket closed error
- solvate and write pdb, psf file.
- Solvate Package
- solvent bands and periodic boundary conditions
- Solvent mixture
- Solvent model other than TIP3 for use with CHARMM FF in NAMD??
- some cluster questions
- Some problem on compiling NAMD
- Some question about Constraint~
- Some questions about TCL
- Some warnings from log file after minimization
- Source code for NAMD
- Source file in the tutorial
- Space environment simulations
- SPC/E Water Model and RigidBonds
- spherical boundary condition
- Spherical Boundary Conditions
- Spring Constant
- start fep calculation
- statistical test
- steepest descent minimization
- steered molecular dynamics docking
- still problems with namdplot
- strange behaviour when running apoa1 on 1 processor
- Stray PME grid charges
- submitting a job in a queue
- Submitting jobs on myrinet...problem
- success with opteron myrinet mpi etc
- successive minimization with different sets of fixed atoms
- surface density of lipid bilayer
- surface pressure/tension
- Surface tension
- Suse 9.0 or Fedora Core 1.0
- switching SMD in execution script?
- Sybyl trajectory
- Symmetry operations
- sync buffer overflow
- system becomes very large when set LangevinPiston on
- System minimization: fail after 199 steps
- Systems of > 100,000 atoms, *.psf files & *.crd files
- TCBG "Hands-On" Workshop on Computational Biophysics in Boston, Dec. 5-9
- Tcl dihedral restraints in CG minimisation
- Tcl forces
- Tcl interface--dynamically changing simulation parameters
- Tcl load
- Tcl loops in configuration files
- tcl question
- tcl script for calculate RMS of MD calculation ?
- tcl scripting interface in namd 2.5 for IBM-SP
- TCL: can't use floating-point value as operand of "-"
- TCL: getting forces
- Tcl: loadtotalforces
- tclForces - addforce to group of atoms
- tcoupling coefficient
- temp coupling coefficients
- Temperature
- temperature "coupling coefficient" in NAMD
- temperature autocorrelation
- Temperature control methods in NAMD
- temperature control question
- Temperature control?
- temperature coupling and pressure coupling
- temperature coupling in NAMD
- temperature question in logfile
- Temperature reassignment problem
- temperature rescaling and canonical ensemble
- test and a short question!
- Thanks a lot
- thankyou
- The angle parameters for CN7 are missing in NAMD?
- the difference between the min_nacl.vel and min_nacl.restart.vel
- The HT-HT-OT angle parameter for TIP3?
- the lastest version of NAMD source
- The psf format conversion
- The vector direction in SMD
- thermodynamic integration and NAMD: soft-core or "separation-shifted" vdw potentials
- Thermostat problems
- three-site carbon monoxide model
- timeout on running namd
- Timestep in restart output
- TIP5P
- TM protein in octane slab questions
- To PME , Do the simulation need a neutral charged system?
- too much rattle
- topology and parameter for acetylcholine
- topology file for compound
- Topology for nano tubes
- torsion angle
- Torsion potential barrier (low?) in NAMD
- Torsional barrier(adding parameters)
- total energy stuck between two levels
- Trajectory file.
- tRNA simulation psf file generation explicit solvent and ions
- Trouble with NAMD on Myrinet
- truncated octahedron boundary conditions
- trying to generate a peptide
- turning off fixed atoms in the middle of simulation
- type of the water molecule
- Tyrocine dynamics came out wrong.
- UNABLE TO FIND ANGLE PARAMETERS FOR HT HT OT
- Unable to Generate PSF file !
- UNABLE TO OPEN .psf FILE
- undefined loops
- undefined symbol errors:__builtin_bzero and _alloca building mpi-ppc-darwin version of namd2.6b1
- Understanding NAMD performance data
- unexpected end with NAMD on quad-dual core opteron machine
- Unit cell coordinates and radial distribution functions
- Unit of force using Haptic in IMD
- Unprotonating GLU, ASP
- unstable simulation with AMBER ff in AMBER!
- Unwrap molecules
- unwrapping dcd trajectory
- Update on Implicit Solvent Models in NAMD?
- Urea and GdHCl parameters
- urestraint
- urestraint ?
- urestraint doesn't work
- Urey-Bradley term?
- user-supplied conformational restraints
- Using an arbitrary tabulated potential in NAMD
- Using checkpoints in simulation
- Using FEP as non-disruptive mutation procedure
- using namd to compute energies
- using restart files
- Vaccum simulation
- Van Der Waals energy
- Variation of results in iterations
- vdwGeometricSigma for OPLS in NAMD 2.6b1 Release
- vectorized NAMD version?
- Velocity after heating
- velocity file of atoms at each time step
- velocity quenching
- velocity unit
- visualizing dynamics output
- VMD scripting
- VMD scripting (Thanks a lot)
- VMD solvate in CCl4
- vmd-l: autoimd on windows
- vmd-l: Autoionize plugin problem
- vmd-l: conformational alignment
- vmd-l: convert DCD files to CRD format
- vmd-l: convert DCD files to GROMACS .XTC format
- vmd-l: how can I get hole program
- vmd-l: incompatibility between VMD & NAMD for reading Amber crd files
- vmd-l: Interactive Simulations, ligand size limits....
- vmd-l: multiple automated calls to NAMD
- vmd-l: Nanotube Simulations
- vmd-l: Protonated GLU/ASP in PSF generation
- vmd-l: psfgen and xplor topology
- vmd-l: PSFGEN problem
- vmd-l: ptraj
- vmd-l: rmsd problem
- vmd-l: script
- vmd-l: Script for calculating energy of a water molecule
- vmd-l: Sybyl trajectory
- vmdtext and .cshrc.
- vmdtext?
- volume from VMD and NAMD different?
- wallclock and cputime
- Warning in namd output file
- warning messages in psfgen
- warning on unique coordinates
- Warning: 1 margin violations
- Warning: 8 margin violations
- Warning: add bond failed in patch of ACE
- Warning: Not all atoms have unique coordinates.
- warnings during NAMD simulations.
- water box
- water box and system charge
- water box and the procedure
- water box is too small
- Water Box Shrinks
- water density calculation
- Water Sphere
- Weird dihedral error
- What binaries should I take?
- What the result difference between AMD and Intel CPUS?
- What's wrong with my namd2
- What, if no temperatue control specified?
- Where to download the inorganic pdb file
- Why Vmd didn't show the Pt-Cl bond
- Working on cluster to do umbrella sampling
- wrap ions
- wrapping DCD files
- writeback periodic cell info in dcd output
- Writing pdb file.. easier way?
- xplor parameter to charmm
- XPLOR psf format
- xplor to charmm
- XPLOR topology to CHARMM
- xsc file reading and segmentation fault
- xsc information in the dcd file?
- Xserve G5
- your mail
- Z-origin set to zero by Linux/Mac 2.5 binaries, Minimisation
- Zeros at the beginning of each line in the output
Last message date: Wed Dec 28 2005 - 17:21:37 CST
Archived on: Wed Feb 29 2012 - 15:40:15 CST
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