NAMD-L: By Subject
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About this archive
Starting: Fri Jan 01 2010 - 09:55:54 CST
Ending: Sat Dec 31 2011 - 05:23:47 CST
- "Constraint failure in RATTLE algorithm" when restart FEP
- "didn't find VdW parameter for atom type NH3" error
- "FATAL ERROR: Bad global improper count" revisited
- "gradient tolerance" for minimization
- "GroupPressure no" resulting in negative pressure outputs
- "Hands-On" Workshop on Computational Biophysics, March 21-25, 2011, Atlanta, GA, USA
- "Hands-On" Workshop on Computational Biophysics, November 1-5, 2010 & November 29-December 3, 2010 in Urbana, IL
- 'cutting' colvars.traj file
- 'firsttimestep' treated as signed integer ?
- 'Hands-On' Workshop on Computational Biophysics using VMD and NAMD, February 11-15, 2012 in Urbana, Illinois
- 'Hands-On' Workshop on Computational Biophysics using VMD and NAMD, October 17-21, 2011, Bremen, Germany
- (Infiniband-related?) NAMD 2.7b2 (ibverbs x86_64) runtime error during a MD run
- (NAMD2.7b1) loadtotalforces gives output even when there are no forces in system
- (no subject)
- (solved) charmrun: ssh_exchange_identification: Connection closed by remote host
- (âÅÚ ÔÅÍÙ)
- * CGtool force field *
- .colvars.state file in ABF
- .COOR TO PDB FILE
- 1-4 pair generation
- 1us simulation of 80k atom system -- how much gross structure movement is expected?
- 2 Stray PME grid charges detected possible bug 2.7b2
- 4 x Opteron 12-core or 4 x Xeon 8-core ?
- ??: compilation of namd
- [ppl] Compliling NAMD in RedHat
- [ppl] error compiling charm-6.2.2 for bluegenep-xlc
- [ppl] Help Regarding NAMD Application Testing
- [ppl] NAMD at linux on sparc
- [ppl] Regarding Compiling in Redhat linux.
- A "strange" observation during ColVar calculations
- a bundle of coor files
- a cv-smd puzzle
- a gap in flowing water
- A namd2.8b1 bug ?
- A newer version of win32 libraries
- A problem of the forces-tutorial
- a question about modifying the NAMD input file
- a question about NAMD TI
- A question on Jarkynski equation
- Abe versus Lincoln
- ABF & distanceZ projection axis
- ABF & distanceZ projection axis more
- ABF (NAMD 2.7x) speed ?
- ABF - sequence of MD runs
- ABF atom selection
- ABF atom selection question
- ABF calculation using RMSD
- ABF calculations: Jacobian term describing geometry entropy
- ABF colvar error-capped nanotube interaction
- ABF Displacement
- Abf force output
- ABF in various simulations
- ABF non-uniform sampling
- ABF on NAMD 2.7b3
- ABF problem with gyration radius/Cl and Br
- ABF question
- ABF question (sampling and colvars output file)
- ABF questions
- ABF questions (Concatenate output files/force constant)
- ABF reproducibility
- ABF Restart
- ABF results interpretation
- ABF Simulation Crash from TCL script
- ABF simulation with extendedLagrangian on keeps crashing
- ABF with Alpha colvar can't be used on supercomputer?
- ABF: moving system in Z direction
- abf_integrate
- Abnormal EOF Error in Extra Bonds File
- About "alchDecouple" in FEP
- About "equilibrate.conf' of FEP tutorial
- about charmm force field
- About Columb energy of 2 ions in Vacuum
- about conf file
- about D amino acid
- about DCD file format document
- about extrabonds restrain
- About fastest CUDA cards
- about Hydrogen Bond correlation function
- about log file
- About matdcd
- about md in npt
- about NAMD nonbonded routines
- About plumed installation problem in NAMD_2.6_AIX-POWER-MPI
- about protein phosphorylation
- about recentering of namd trajectory
- about rigid bonds
- About RMSD based PMF's
- About the err of "Constraint failure"
- About the err of "distanceZ"!
- About the solvate package
- About viscosity calculation
- Accelerated MD documentation?
- Accelerated MD with membrane embedded proteins.
- Accelerated MD: question about dual boost mode
- Accelerated MD?
- Accelerated Molecular Dynamics
- Acceptance ratio of REMD simulation
- Accessing Colvars Within NAMD TCL
- accuracy of measurement
- Acetyl group patch for lysine residue
- Add bonds and topology file problem
- Adding extra bond
- Adding special VdW parameters
- ADENOSINE-5-DIPHOSPHORIBOSE topology
- Advice on buying GPUs
- Advisable limit on the number of quadrants a 2D ABF simulation can be split.
- alchDecouple
- Alchemical calculations in CUDA version of NAMD?
- Alchemical FEP tutorial files
- alchemy FEP query
- aligning two molecules by principal axes of inertia using measure.c
- Allowed CMAP dimensions
- Allowed CMAP dimensions in NAMD
- Alpha P.M.F. with NAMD 2.8
- alpha pmf
- altering residues in .pdb files
- Am I using the right version for accelerated MD?
- AMBER force field in NAMD
- Amber topology in CUDA NAMD - can it be done?
- AMD Multicore + CUDA Benchmarks, are them ok ?
- AMD-PhenomII-1075_GTX470 NAMD-CUDA performance
- ammonia to methane
- ammonia to methane/ c/o Jerome Henin
- ammonia to methane/DISREGARD this post-changes to files below make methane work now
- an important question for equilibration script
- analysis of dcd
- Analysis of Results of only Lipid Bilayer Simulations
- analysis question
- Andres Morales sent you a little gift
- Angle in parameter file
- angles
- Announcement: TCBG workshop at Pittsburgh Supercomputing Center May 10-14, 2010
- anomalous behaviour of ASPP and GLUP during MD run
- Another PSF question...
- apoa1 bencmark for 2.7 MPI compiled
- apologize for the typo
- Applying a positional restraint with colvars module
- Appropriate dcdfreq
- are tclForces included in minimization?
- Area per lipid error
- Asking for some sample PDB and PSF files of carbon nanotube
- Assertion failed in file @ KRAKEN
- Assigning partial charges in topology file
- atom charges for protonated carboxyl termini
- Atom movement within a range of Z value
- atom select within hbond analysis
- atom type
- Atom type for protonated pyridine N
- Automatic GPU selection in NAMD ?
- Automatic PSF Builder Problem
- AW:
- AW: .COOR TO PDB FILE
- AW: about extrabonds restrain
- AW: aligning two molecules by principal axes of inertia using measure.c
- AW: AMD-PhenomII-1075_GTX470 NAMD-CUDA performance
- AW: Automatic GPU selection in NAMD ?
- AW: AW:
- AW: AW: about extrabonds restrain
- AW: AW: Automatic GPU selection in NAMD ?
- AW: AW: AW: AW: namd-ibverbs fails to start
- AW: AW: AW: NAMD crashes with OpenMPI/OpenMX
- AW: AW: AW: namd-ibverbs fails to start
- AW: AW: AW: question about wrap atoms to its original coordinates
- AW: AW: NAMD crashes with OpenMPI/OpenMX
- AW: AW: namd-ibverbs fails to start
- AW: AW: question about wrap atoms to its original coordinates
- AW: AW: Running NAMD parallel on two machines with 3 CUDAs
- AW: AW: save the last frame as a pdb file using dcd file
- AW: Batch Mode MD simulation Script for NAMD
- AW: cell size
- AW: compilation of namd
- AW: Constraint failure during equalibration
- AW: Corrupt dcd files
- AW: CUDA on GPU Cluster
- AW: CUDA simulation memory usage
- AW: deca-Ala simulations with different cutoff produce different results
- AW: Error with "namd"
- AW: free energy of binding
- AW: glycosaminoglycan with GLYCAM06 in amber format
- AW: Ib version and nodelist
- AW: Infiniband and commodity hardware
- AW: installing namd on ibm cluster (powerpc)
- AW: Letzte Hilfe
- AW: max number of CPU PEs per GPU?
- AW: Minimization doesn't stop when converged
- AW: Minimization is taking a lot of computing time.
- AW: Multinode NAMD CUDA GPU Selection
- AW: Multiple Runs in a Single Conf File
- AW: NAMD crashes with OpenMPI/OpenMX
- AW: Namd-I: namd compiling problem
- AW: namd-ibverbs fails to start
- AW: nvidia cuda driver version
- AW: patch becoming too small
- AW: Peptide planarity Dihedral angle restraints
- AW: Problem with NAMD 2.8 (but not in 2.7) : Endless loop repeating "The last position output ..."
- AW: question about wrap atoms to its original coordinates
- AW: Reading files for multiple threaded simulations
- AW: Running NAMD parallel on two machines with 3 CUDAs
- AW: save the last frame as a pdb file using dcd file
- AW: script for equilibration
- AW: Sticking TIP4P water molecules AMBER
- AW: stochastical boundary conditions in NAMD
- AW: temperature-TS with NAMDplot
- AW: update: segmentation faults with AMBER topology and RAMD tcl scripts
- AW: water equilibration
- AW: water is forming bonds between oxigens
- AW: Win64-MPI
- backbone restraints
- Bactenecine
- Bad atom ID in extra bond file
- Bad Global Exclusion Count Errors in (Relatively) Simple System
- Balancer and singularities ...
- Batch Mode MD simulation Script for NAMD
- Benchmark for NAMD2.7 (curent version)
- benchmarking on Cray XT4
- berendsen thermostat
- Best tool to use to generate a custom (patched) polypeptide PDB?
- beta column
- bigdcd file help
- Bin Coordinate file to pdb
- binaryrestart/binaryoutput problem
- Bioinformatics Symposium at C-DAC, Pune
- blank between nanotube and the bulk water
- Blue Waters
- bond lengths angles in namd
- bonded FAD topology file
- Bonds are too long after simulation
- BOUNCE namd-l@ks.uiuc.edu: Message too long (>40000 chars)
- Boundary potential of colvar alpha not working?
- Bringing UMA-type mainboards to TESLA
- Build .pdb and .psf after coarse graining results in errors
- build a layer
- build a wall
- build nanoparticle
- building a MARTINI bilayer
- Building PSF file for protein with ions
- calculate side-chain dihedral/torsion angles
- calculating energy term from extrabonds
- Calculating interaction energy in NAMD
- Calculation of distance traveled by an atom
- Calculation of IR spectra using VMD IRspec Plug-in
- calculation van der Waals force field parameters
- Can AMBER topology be used in NAMD-CUDA?
- Can DCD trajectory files contain only protein but water surround
- Can I do protein-ligand docking using NAMD?
- Can I set a range to limit the ABF
- Can paratools really parametrize a structure? Is it really finished?
- can RHDO crystal shape works in NAMD
- can we run FEP calculation in water sphere?
- CAN'T FIND BOND PARAMETERS FOR BOND C - CPB IN PARAMETER FILES
- Can't find C-PDB bond parameters
- Cannot find bond parameters
- Carma v.1.0 released.
- Carma v.1.1 released.
- Cartesian vs dihedral angle space PCA
- CatDCD installation
- Cationic Dummy Atom models
- cell basis vector restart
- cell size
- cellBasisvectors/.xsc fixing/colvars while running amber ff
- Center of Mass Harmonic Potentials
- CG parameterization problem
- CG parameters from dcd file for protein CG modelling
- CG-MD high electrostatic energy values
- CG_MD temperature
- change force field in NAMD
- change solvent
- Changing functions without recompiling
- changing solventDielectric in GBIS
- Changing the Potential Energy Function
- Channel flow equilibration
- charge calculation
- charges in psf and in namd (or vmd)
- CHARM parameter file needed for simple organic molecules like Methanol, Formamide, Chloroform, TCE, Toluene
- charmm 19 parameters
- Charmm carbohydrate force field
- CHARMM FF parameters for O2 Gas
- charmm force field
- CHARMM General Force Field (CGENFF)
- CHARMM Lorentz-berthelot mixing rules
- Charmm parameter for H2 gas
- Charmm parameters for
- CHARMM parameters for Mn 2+ ion
- charmrun constantly hanging
- Charmrun: error on request socket--
- Check out my photos on Facebook
- cholestrerol
- claen water
- Cluster on commodity hardware
- clustering of trajectory
- CMAP dimension limited to 24 dimensions
- CMAP dimensions in NAMD
- CMAP in NAMD output
- CmiAbort+0x5f
- coarse graining
- Coarse Graining problem resolved
- Coarse Graining setup question
- coarse-grained MD
- coarse-grained model building
- Coarse-Graining MD don't work perfect as expected
- Coarse_Graining tempetrature
- collective variable calculation from dcd file
- coloring method in VMD
- colvar and tclForces with CUDA
- colvar atom syntax
- colvar error
- colvar for PMF calculation
- colvar module question
- Colvar on 2.7b2 win vs Linux MPI instalation
- colvar restrain of water in lipid system
- colvar: atom group defn. fails
- colvar: coordnum output
- Colvars "tilt" component force constant units for WHAM
- Colvars and COM restraints for protein+membrane; plus a minor bug
- colvars don't run with minimization ...
- colvars error running ABF
- colvars fixes
- Colvars in NAMD 2.7b4
- colvars orientation problem appears in 2.8 only?
- colvars PMF history problem
- colvars, discontinuous rotation
- colvars-history file
- colvars: Error: in parsing "centers"
- colvars: free energy change with rmsd
- Colvars: Using "Alpha" Component
- colvarsInput filename problem
- combining metadynamics simulations
- combining thermodynamic integration with replica exchange in NAMD
- Comparision of GPU and multi-CPUs version of NAMD
- compilation of namd
- Compiled Windows HPC version.
- Compiling NAMD 2.7 with the PLUMED patch
- Compiling NAMD for CUDA
- compiling namd gpu
- Compiling NAMD on Cray XE6
- Compiling Namd on MAC with Cuda
- Compiling NAMD under SGE and OpenMPI
- compiling NAMD w. infiniband
- Component distanceZ-ABF
- Computing interaction energies in namd
- Computing several pair interactions
- concatenate pmf files in colvars
- conf file script ( help needed )
- configuration file
- Conjugate gradient reference
- Consecutive Simulations
- Constant pressure
- Constraint failure during equalibration
- Constraint failure in RATTLE algorithm for atom 268
- Constraint Failure in SMD simulation
- Constraint failure; simulation has become unstable
- Constraint failures and TI electrostatic calcs
- Constraints on the plane and on the atom positions (in the same simulation)
- constraintScaling to gradually release harmonic restraints during minimization
- Control DCD file
- control distance between solvent and solute
- Controlling fans on a GTX 560 ti
- convergence and stability of simulation
- convergence of ABF
- convert pdb format to normal pdb format
- coordinate not the same between the input and frame 0
- coordinates and cells
- coordNum colvar with dummyAtom
- correlation functions
- Corrupt dcd files
- Could namd support the ATI-GPU
- Could namd use the method ONIOM of Gaussian?
- couldn´t find rsh program
- Coulomb 1-4 interactions
- Coulombic component of configurational energy
- counting h-bond in system with vmd
- CPU GPU comparison
- CPU usage when exec function is used
- cpu-gpu vs cpu
- crash
- Crashing ibverbs binary of NAMD_2.7b2
- creating .psf file for a nanotube
- Creating a NAMD Shared Library -> Undefined Symbols in Charm libs
- creating an output file from a dcd file
- CT1 terminal patch for THR
- CthCreate failed to create fiber
- Cu+2 parameters
- Cube vs. Truncated Octahedron Performance
- CUDA compiled code for Windows HPC
- cuda error cudastreamcreate
- cuda error cudastreamcreate. SOLVED (probably)
- CUDA error in NAMD 2.7: Increase MAX_EXCLUSIONS
- CUDA error memcpy to exclusions: invalid argument
- CUDA limitations
- CUDA on GPU Cluster
- CUDA simulation memory usage
- CUDA-NAMD hangs -- check the Northbridge temp!
- Current status of polarizable force fields in NAMD
- Custom CHARMM forcefield usage problem
- Dangling Bonds?
- dcd
- dcd files
- dcd to trr using catdcd
- dcd]
- Dear friend
- Debug NAMD with CharmDebug
- deca-Ala simulations with different cutoff produce different results
- Definition of two colvars for ABF
- Definitions of certain routine names in source
- degrees of freedom
- Denaturation via increased temperature
- Denied permission on dcd file preventing simulation
- Density Profile in VMD
- Deprotonated Lys
- determining force constant in exterbonds (harmonic potential)
- Development plan of NAMD?
- dextran and or poly-D-glucosamine topology
- Dielectric Constant
- Difference between cwd and cd
- difference between run and minimize
- Difference between the two Dowsers
- Differences between ABF and metadynamics
- differences in multiprocessor energy minimization results
- Different Dielectric constant value for different segment
- Different types of constraints at the same time
- different values of "1-4scaling" in a system
- different velocities problem
- Dihedral angle energy in silica block
- Dihedral angle potential energy function
- Dihedral parameters for side-chains?
- dihedral rotation with ABF
- dihedral terms for a parameter file
- discrete energy value after restart
- dissociated quartz SiO2 groups in surface
- Distance Analysis for Constant Force Pulling for kinesin neck linker
- distance calculation between atoms of two segments
- distance colvar
- Distance constraint
- Distance Restraint
- Distance XY-colvars
- distanceXY colvar-ABF
- distortion of some bonds during structure preparation
- Distribute Points Evenly on Surface of a Sphere
- Dividing a 2D ABF simulations into regions (on nodes with different speeds)
- DNA terminal Patch / How could I retain the primes in DNA
- Dock a metal ion into a peptide/protein
- Does "rigidbond off" work instead of "rigidbonds none"
- does any body have the parameter file for aldehyde group?
- Does CHARMM stabilize alpha helices?
- Does GB Implicit Solvent handle explicit ions?
- Domain error ParseFEP
- Dowser
- Dowser with RESIDUE LYR
- DPPC membrane
- Dreiding parameters
- Drift of the center of mass of lipid bilayer
- Drude polarizability parameters
- dual all-atom/coarse grain simulation
- dummyAtom-ABF
- duplicate residue key ALA will be ignored
- electric field unit conversion
- Electrostatic Potential Problems, WRT Minimizations
- electrostatic vs van der waals
- energy jump between minimization and simulation
- energy jump running a simulation after minimization
- Energy minimization
- Enhance electrostatic interactions?
- Enthalpy calculation
- Enthalpy calculation from NPT simulation
- Epsilon, Rmin for copper ions
- equilibrate the system in NPT
- equilibrate water molecules
- Equilibration
- Equilibration - NVT & NPT
- equilibration script from restart files
- Equilibration when splitting an ABF calculation
- Errata to: Update to CUDA error in NAMD 2.7: Increase MAX_EXCLUSIONS: problem persists and CPU-only MD scales poorly
- Erratic behavior of TclBC in parallel
- error
- error : atom moving too fast
- error codes: 255
- error compiling charm-6.2.2 for bluegenep-xlc
- error during charm-6.1.3 building
- Error in configuration file
- Error in running minimization
- error in scripting
- error in the orientationAngle
- error of the energy output when equilibration
- Error on closing binary file
- Error when run Replica Exchange Method on Ranger
- error while running config file
- Error while using larger timesteps in Coarse grained Simulation of Polymer
- Error with "namd"
- Error with tclBC to induce shear flow
- Error with ubqp.pdb in NAMD tutorial
- Error: atom group "group1" is set, but has no definition
- ERROR: Atoms moving too fast with RBCG model
- ERROR: Atoms moving too fast;
- ERROR: Constraint failure in RATTLE algorithm for atom
- ERROR: CUDA-enabled NAMD requires at least one patch per process
- error: expected floating-point number but got
- Error: keyword "group1" is not supported, or not recognized in this context.
- Error: This application has requested the Runtime to terminate it in an unusual way: Please contact the application's support team for more information" after specifying the namd2.exe path
- Evaluated heat capacities via NAMD are larger than experimental values
- evaluating energy in a trajectory of variable box size?
- ewald method
- ewald self energy
- example psf and pdb files for simulations with tip4p
- Excluding interactions?
- expansion of solvation box at high temperature
- expect NAMD survey emails this week
- Explicit Solvent Sytem (40% Ethanol + 60% Water)
- Explicit Water System Condensing
- extending namd / shared library build (UNCLASSIFIED)
- external forces
- Extra bonds-ABF
- Extract trajectory from replica exchange simulation
- Fail to Run VMD
- Failure to run namd-cuda with gtx-470
- Fatal Error by charmc - Compiling NAMD_2.7b2_Source
- Fatal Error Periodic cell has become too small for original patch grid
- FATAL error when run Replica Exchange Method on Franklin
- Fatal error when running ABF simulation
- FATAL ERROR: ABNORMAL EOF FOUND-buffer
- FATAL ERROR: Asymmetric water molecule found??? This can't be right.
- FATAL ERROR: Bad global angle count!
- FATAL ERROR: CAN'T FIND CROSSTERM PARAMETERS FOR CC NH1 CT1 C NH1 CT1 C NH1
- FATAL ERROR: Couldn't open DCD file equil0.dcd: No such file or directory
- FATAL ERROR: Due to a design error, GlobalMasterServer does not support individual atom requests from multiple global force clients on parallel runs.
- FATAL ERROR: Low global exclusion count! System unstable or pairlistdist or cutoff too small.
- FATAL ERROR: Setting parameter fixedAtomsFile from script failed!
- FATAL ERROR: UNABLE TO FIND ANGLE PARAMETERS FOR CT2 CT1 CT2 (ATOMS 107 98 100)
- FATAL ERROR: UNABLE TO FIND ANGLE PARAMETERS FOR HT HT OT
- FATAL ERROR: UNABLE TO FIND BOND PARAMETERS FOR C H (ATOMS 2 1)
- FATAL ERROR: Unable to open binary file
- FATAL ERROR:BAD GLOBAL EXCLUSION COUNT:Please help
- Feature request for the colvars module -- TCL syntax
- FEP - Protein binding to Membrane surface
- FEP and GPU
- FEP calculation is doing nothing
- FEP for GLY and PRO Mutations
- FEP substrate transformation with common moiety
- FEP VdW and electrostatic decoupling parameters
- FEP with flattened free energy surface?
- FEP yields the same results for forward and backward computation!
- Fermi NVidia
- FFTW and NAMD problems during compiling on BluegeneL
- fftw libraries for ppc
- file writing stopped
- Filtered mail?
- Final production run in MD
- finding appropriate topology file for polymers
- finding water around protein
- firsttimestep in NAMD
- Fix atoms-Colvars
- Fixatoms minimization problem!!
- Fixed COM
- fixing group of atoms, Proper for manipualation
- flashmob namd
- flexible-cell constant pressure not supported in CUDA
- Flushing memory into output file
- for your suggestions on Pressure Control of transmembrane protein (GPCR)
- Force constant for Umbrella Sampling
- Force constant scaling
- force field
- force field for 2-methyl-2,4-pentanediol (MPD)
- Force field for PDMS
- Force field for replica
- force field for replica exchange with NAMD
- force question
- Force Vector Between Two Atoms
- ForceConstant in Umbrella Sampling
- Forcefield for simulating peptide with heparin!!!!
- forces on fixed atoms
- Format of namd restartfile *.coor, *.vel) (2nd try ;) )
- formyl and ethanolamide parameters and topology
- Free energy calculation yields strange results
- free energy changes of one subunit
- free energy of binding
- free energy perturbation
- Free energy perturbation (FEP) hybrid pdb file
- Free-energy perturbation in NAMD: Evaluation of electrostatic and van der Waals terms
- freeEnergy parsing error
- fullSamples in ABF: applied at restart?
- Fwd: "cuda error cudastreamcreate",
- Fwd: about md in npt
- Fwd: AMD-PhenomII-1075_GTX470 NAMD-CUDA performance
- Fwd: binaryrestart/binaryoutput problem
- Fwd: Coarse Graining Problem
- Fwd: cuda error cudastreamcreate. SOLVED (probably)
- Fwd: electric field unit conversion
- Fwd: error : atom moving too fast
- Fwd: Fwd: hi
- Fwd: Generating .tpr file using NAMD files
- Fwd: hBond component in colvars and patching
- Fwd: help to improve the script to predict mean square displacement
- Fwd: hi
- Fwd: hi all
- Fwd: Incompatibility between colvars and tclforces?
- Fwd: Installing NAMD on windows
- Fwd: Keyword "lower" not supported...colvars
- Fwd: membrane moving up in simulation box
- Fwd: minimization problem
- Fwd: nvidia 275.09.07 driver. SOLVED, NO DRIVER PROBLEM
- Fwd: phosphotyrosine
- Fwd: problem regarding charmm parameter file of carbon nano tube
- Fwd: ramd firstRamdAtom
- Fwd: ramd seed
- Fwd: RAMD Setting parameter TclForces from script failed
- Fwd: Re : Setting up a membrane simulation
- Fwd: reading prameter file
- Fwd: restrain on COM
- Fwd: rigid bonds
- Fwd: Solved stream files and paratool
- Fwd: STRIDE Question from article "Interpeptide interactions induce helix to strand structural transition in Abeta peptides"
- Fwd: suitable motherboards for both graphical visualization and NAMD-CUDA computation?
- Fwd: Wrong exit from RAMD runs
- g(r) calculation for CNT
- GBIS and ABF
- GBIS and hydrophobic solvation
- GBIS and hydrophobic term, in replay to Jerome and David discussion
- GBIS not compatible with CUDA at this time
- GBIS on GPU?
- GBIS question and possible Bug for colvar "outputSystemForce" declaration in NAMD CVS-2011-03-03
- GBIS synamics
- GeForce vs Tesla GPUs for high performance computing
- Generalized Born calcs
- Generalized Born implicit solvent model in 2.8b1
- Generate missing atoms of a coarse grained structure
- Generate psf files from Scott Feller's lipid coordinates
- Generating .tpr file using NAMD files
- Generating binvelocities, bincoordinates, and extendedSystem files (AMBER)
- Get number of timesteps from DCD via script
- Get restart file (restart.coor) from DCD
- get total force on a group of atoms within GlobalMasterSMD
- getting desired angle
- Gibbs potential
- global and internal motion of protein
- glycosaminoglycan with GLYCAM06 in amber format
- Gold nanoparticle and 1-octanethiol
- GPRESSURE becomes nan in TIP4P simulation
- GPU heavy models?
- GPU-CPU small-scale machine for NAMD
- gradient tolerance
- grid-based correction map
- gromacs analysis tools
- H-bond and salt bridge between protein dimer
- harmonic constraint when equilibrate the system
- hBond colvars and patching
- hBond component in colvars and patching
- headgroup area calculation
- heat annealing conf file
- Heating /Equilibration
- heating and binvelocities
- Heating in NAMD
- Heating in NPT
- Helix tilt
- Hello
- Hello!
- help
- Help building a desktop for namd
- help in a FEP restart?
- Help in FEP backward/reverse calculation
- help in FEP calculations : analysis/confirmation of results
- help in FEP calculations_binding free energy difference between 2 inhibitors
- Help in reverse Free Energy perturbation - hysteresis
- help needed
- Help required for nanoscale simulation
- help whit distance restraint
- Help With colvars/abf Please
- Help with cys unprotonated
- help with the equilibration script
- Help: NAMD on cluster; nodes reject multiple connections
- HEME and Cystein instead of His
- Hepl whit colvar subrutiene
- HETATM vs ATOM in .pdb file
- hexane
- hi
- hi all
- Hi, I am a new user of Namd, and I met some problems using increment of temperature during simulation
- Hi: some doubt about nvt and npt equilibration
- high atom velocity
- high pressure
- High RMSD in Coarse Grain Simulation of Protein
- High RMSD of Coarse grain Protein
- highthroughput NAMD
- Hints for building namd2.8 on charm++ ibverbs layer?
- how best to build a GPU-accelerated desktop machine for NAMD?
- How can I connect different structures between them using VMD and NAMD?
- How do I connect the non-overlwindows of ABF's results?
- How I can insert de harmonic restraint?
- how obtain .xst form .dcd file?
- How to analysis RAMD data?
- how to apply different temperature simultaneously to different atoms in the same system
- How to calculate Binding Free energy in NAMD
- How to calculate binding free energy of a protein-DNA complex by using NAMD?
- how to calculate partial charge for ligand based on CHARMM principle?
- how to cenvert NAMD binary coordinate file to text file
- How to confirm water box is big enough?
- How to convert the GROMOS parameter unit into charmm22 style
- how to convert X_PLOR to CHARMM?
- how to define the numsteps in ABF or metadynamics simulation?
- how to ensure molecules adopt their favor orientations in SMD simulation
- How to evaluate the area per lipid and thickness of the lipid bilayer in a membrane-protein system?
- How to generate the tcouple file for NAMD runs?
- how to generate the topology and parameter file for ligand
- how to generate topology and parameter file for ligand
- how to generate transparent figures?
- how to get .coor .vel and .xsc for a .dcd file
- How to get information of computing time for LJ calculation and pair list generation
- How to get PMF from SMD with colvars
- how to get the energy in vacuum of a molecule in NAMD
- how to get topology and parameter file for ligand
- how to improve the occupation of GPU with NAMD-2.7b3-CUDA
- How to restraint angle in NAMD
- how to save a DCD file without water in NAMD ?
- how to save a DCD file without water in NAMD: COMMAND LINE
- How to set improper dihedral for trans-double bond.
- how to set pH
- How to set the right PME parameters for amber's prmtop and inpcrd files?
- How to simulate a charged surface
- How to solve the out of cell box for long time in Periodic Boundary Conditions?
- how to submit job on a HPC equipped with infiniband
- How to use harmonic restraint parameter for 2 selection of atoms
- how to use variables in colvar configuration file
- how to visualize an alchemical FEP transformation??
- How to write a dcd in fortran?
- How to write gradual heating config files
- how to write out the dcd file by vmd python command?
- how to write the bond across the cell boundary
- How were the output files of the Replica Exchange Method sorted?
- html manual 2.8, ref 46 and some GBIS questions
- hydration in membrane-protein simulations
- I can patch namd for amber ff on GPU
- I M wants to share "legis_2011" with you
- I need help with this
- Ib version and nodelist
- IBverbs charmrun problem
- image centering problem
- IMD VMD NAMD adding frames
- Implementation of Martini CG FF in NAMD
- implementing RBCG
- Implicit solvent
- implicit solvent and cuda
- implicit solvent job error in NAMD2.8b1
- Implicit solvent simulation
- implicit solvent with iapbs
- Importance of the Topology File, .rtf, and Other Files
- impose restraint on the internal coordinate of protein
- improper angle
- Impropers in Charmm and OPLS
- in NAMD tutorials: why "HSE" instead of "HSD"?
- Incompatibility between colvars and tclforces?
- Incorrect Atom Count in binary file
- increasing MAX_EXCLUSIONS
- Infiniband and commodity hardware
- Info: Attempting to read FFTW data from FFTW_NAMD_2.7b1_Linux-Itanium-MPI-Altix.txt
- infrequent rattle failure with charmm36
- initial structures for md simulations
- input file for memory optimised version
- Input/output error
- install NAMD 2.8 v
- installation of namd
- Installation of NAMD & charm - fatal errors
- installation of namd in parallel mode
- installation of namd without tcl and fftw
- Installation problem on Win64
- installing namd on ibm cluster (powerpc)
- Interaction energy difference
- Interaction potentials W-S
- interaction-energy
- Interactive MD driver/controller software no longer in beta
- Interface analisis
- Interfaces in NAMD
- intermittent non-execution of NAMD on tesla
- interpretation of timing data in output
- Invitation to connect on LinkedIn
- ion concentration in residue-based coarse-grained model
- Ionize script
- Ions conversion from atomic model to coarse grained model
- Iron Oxide and Arsenic
- iron sulphur cluster parametrization
- Is it possible to print out the force of one specific atom?
- Is it possible to run replica exchange simulation on BlueGeneL?
- Is the DCD file size consistent for consecutive runs?
- is there any difference between non-constrained equilibrium and normal MD production?
- Is there any difference between SMD and tclForces?
- Is two colvars file output possible during single simulation (ABF/2.7b)
- isopropanol parameters?
- Issue attaching to nodes
- Issue with Load Balancing
- Issue with NAMD Not understand
- Jarzinsky's equation
- Job Offer
- Job restart
- Job scheduling (managing) software recommendation
- job script for Kraken
- job termination
- jobs get stuck using NAMDv2.7 and stop producing output in the log-file
- Joining PSF Files
- K25 NIH award
- Keeping rigidBonds during Minimization
- Keyword "lower" not supported...colvars
- Langevin Buffer Region
- Langevin Damping = 0?
- Langevin process in NAMD tutorial
- langevinhydrogen on with rigidbonds water
- langevinTemp and system temperature
- large load rate using implicit solvent
- Large protein translation during minimization
- last call for 2.7b3 bug reports!
- last frame and restart are different
- Least squares fitting of frames of trajectory
- lengthening time-step with constraints causes RMSD "jump"
- LES dcd file split
- ligand parameters
- Lingand Unbinding using SMD
- Lipid and protein interactions
- Lipid as residues topology
- Lipid bilayer equilibration: Periodic cell has become too small for original patch grid!
- lipids moving
- LJ correction in NAMD2.7b3
- Loadleveler Script on Bluegene for NAMD
- Local elevation method in NAMD?
- Logfile flooded with "The last position output [...]" when IMDon is used.
- looking for topology and parameters of methamphetamine
- low dielectric constants in GBIS
- Low global exclusion count
- Low global exclusion count errors
- Low temperature Molecular Dynamics
- Lowe-Andersen thermostat
- Magnesium Ions Placement
- mainboard-power source for GPU
- Margin Value in NAMD
- MARTINI parameters and Bead definitions
- max number of CPU PEs per GPU?
- maximum number of atoms per patch
- MD condition
- MD simulations increasing electrostatic potential of a certain residue
- mean square displacement
- membrane equilibration
- membrane moving up in simulation box
- Membrane protein simulaton
- membrane simulation and mobility of lipids - blocking ion channel
- membrane simulation at high Temp
- membrane simulation Constraint failure in RATTLE algorithm
- membrane simulation ERROR rattle algorithm
- Membrane simulation, Box X,Y enlarge, Z shrink and membrane thickness shrink
- membrane system
- membrane tutorial.
- Membranes
- memory allocation failed on processor 0
- Memory leak and crash before first step
- Memory leak patch
- metadynamics combined with PCV
- metadynamics simulations slow down and down
- Methanol - Autocorrelation of total dipole moment
- Minimisation algorithm
- minimization and gradient trend
- Minimization at higher temperature
- Minimization convergence
- Minimization does not converge
- Minimization doesn't stop when converged
- minimization gradient question
- Minimization is taking a lot of computing time.
- Minimization messes up C terminal
- minimization problem
- Minimization problem on cluster
- MINIMIZER SLOWLY MOVING 810 ATOMS WITH BAD CONTACTS DOWNHILL
- mininization do not go on
- Mirror Image Energy Discrepency
- Missing angle parameters CT3 CT3 CT3
- Missing angle parameters NH1 CT1 NH1
- Mixed TIP3/TIP4 Waters
- MMTools
- MMTools for analysis
- mmView - a tool for mmCIF exploration
- Model system spherical sieve
- modification of CHARMM force field
- Modification of Colvar Module Components
- modify NAMD code for Lee-Edwards boundary conditions and compute stress tensor
- Modifying a peptide and introducing residues
- modifying velocities within global master
- Molecule2.C
- monitoring instantaneous kinetic energy of a subsystem
- monolayere
- MOnte carlo simulation
- morse potentials in NAMD revisited
- Moving an atom 1A0 in one timestep then running MD for 10,000 timesteps while holding that one atom fixed
- moving inner wall of nanotube with outer wall fixed
- msd calculation for lipid bilayers
- Multi node run causes "CUDA error cudaStreamCreate"
- Multi-step MD in a single .conf file
- multilevel summation in NAMD
- Multinode NAMD CUDA GPU Selection
- Multiple dihedral parameters in X-PLOR format
- Multiple Runs in a Single Conf File
- Multiple runs of NAMD highly take fluctuating times
- multiple trajectories
- multiplicity of dihedrals
- Multiplicity of Parameters for dihedral bond exceeded
- multistep minimization with different constraint
- mutation of DNA
- My benchmark results with TeslaC2050
- my problem was solved
- Mysterious Formation of Solvent Spheres
- Na ion, Cl ion in TIP4P
- NADPH topology
- NAG simulation problem with CPS
- namd ( please help me!!! )
- NAMD + Plumed on Abe
- Namd / gromacs
- Namd 2.6 on ubuntu 9.10
- namd 2.7 iverbs error 93620 attaching to node
- NAMD 2.7 performance issues and Questions about Compiling
- NAMD 2.7 released
- NAMD 2.7/2.8b1 and BlueGeneL
- NAMD 2.7/2.8b2 stuck - [0] processControlPoints() haveControlPointChangeCallback=0 frameworkShouldAdvancePhase=0
- NAMD 2.7b1 distanceDir
- namd 2.7b2 or later - amberff/prmtop causes segfault during startup phase
- NAMD 2.7b2 versy slow on multiple nodes
- NAMD 2.7b3 released
- NAMD 2.7b4 released
- NAMD 2.8 job submission script for queenbee
- NAMD 2.8 job submission script for queenbee: ManyJobs
- namd 2.8 new feature
- NAMD 2.8 on Cray XE6 segfaulting
- NAMD 2.8 released
- NAMD 2.8b1 released
- NAMD 2.8b2 released
- NAMD 2.8b3 released
- namd and Fedora14
- NAMD and Gromacs
- namd at ranger(tacc)
- NAMD cal with AMBER forces: Polarizable parameters in AMBER
- NAMD cell dimension increasing in Z direction, problem with periodic cell
- NAMD chares
- NAMD checkpoint mechanism.
- NAMD complain about gromacs ff parameter ATOMTYPES definition
- NAMD CONFIG FILE::
- NAMD crashes when writing restart file and dcdfreq is 1
- NAMD crashes with OpenMPI/OpenMX
- NAMD CUDA
- NAMD CUDA error message
- NAMD Cuda NBFIX Terms
- namd cuda with geforce 470 (fermi) gpu fatal error at runtime
- namd development mailing list?
- NAMD energy plugin
- NAMD Energy types
- NAMD error message
- NAMD FEP - Bad Hydrogen group size
- NAMD FEP and GPU
- NAMD feture request
- namd files
- NAMD for windows cannot run correctly according to namd tutorials
- namd force field
- NAMD ibverbs not working on new cluster
- NAMD in TACC lonestar
- NAMD initial coordinate file
- namd install
- NAMD installation
- namd job crashed
- namd log file
- NAMD on AMD Istanbul versus intel Nehalem with infiniband
- NAMD on GPU
- NAMD on KRAKEN
- NAMD on linux
- NAMD on PS3
- NAMD on Ranger
- NAMD on Ranger at Teragrid
- NAMD on Shared Memory (Altix UV 1000)
- NAMD OPLS Parameters
- NAMD Pair Interactions Finite Box Size Correction
- NAMD parralel processor windows
- NAMD question
- NAMD regression test suite?
- NAMD running error
- NAMD running on windows HPC question
- NAMD speed on MPICH2 Ubuntu 64 bit Cluster
- NAMD stalled at startup phase 0 when working on a large numbr of processors
- NAMD starts AMBER calculation only from 3rd run
- NAMD terminates prematurely without error.
- NAMD time connect out on multi-computers
- namd trouble
- NAMD Tutorial Problem
- Namd using Charmm restart files
- Namd with Amber ff for RNA minimization
- NAMD with GPU error : "Number of VDW types exceeds CUDA LJ_TABLE_SIZE"
- NAMD with missing residues
- NAMD with Replica Exchange Simulations on Teragrid
- NAMD with TIP5P water
- NAMD with two GPUs
- Namd-1: problems using increment of temperature during simulation
- NAMD-CUDA benchmarks, dual GTX295, dual Xeon Nehalem system
- NAMD-FEP tutorial-alchemify problem
- Namd-I: A question about constant force pulling of a group of atoms
- namd-I: cionize problem in vmd
- Namd-I: Implicit solvent problem
- Namd-I: namd compiling problem
- namd-I: Problems with Namd coarsegrain and Gromacs top file
- namd-ibverbs fails to start
- NAMD-l: energy jump between minimization and simulation
- NAMD-l: Get the PDB file from Steered Molecular Dynamics output files
- Namd. Small molecules
- NAMD/metadynamics
- NAMD/VMD Research Programmer Position available
- namd2 still works but without any new messages in log file
- NAMD2.7 on BluegeneL hang at "LDB: Central LB being created..."
- NAMD2.7/MEtadynamics simulation analysis disparity
- namd2.7b3 vs namd2.7b2
- namd2_ti.pl Modification of non-creatable array value attempted, subscript -49999
- NAMD_2.7_AIX-POWER-MPI
- NAMD_CVS_Source
- NAMDenergy calculations for nucleic acid systems
- NAMDenergy electrostatic energies
- NAMDEnergy Plugin - setting PMEGridSize / mesh density
- NAMDEnergy: FATAL ERROR: Please add +idlepoll to command line for proper performance.
- Namdstats.tcl
- NAMDv2.7 stops producing output in the log-file--any help?
- NANMA free energy surface vacuum map problems
- NBFIX and cuda
- NBFIX for carbonyl atoms and potassium ions -- User Defined Force -- CUDA
- NBFIX support in CUDA NAMD
- NCS
- Need help preventing hydration of the lipid-protein interface in my system
- Net forces on each atom can be written to PDB in NAMD 2.8b1
- Network version gives inconsistent wall clock timings
- New collective variable: biolRel
- New colvar feature request -- angleXY
- new error in NAMD2.8b1 with fixedAtoms
- new NAMD user ABF setup question
- New NAMD version 2011-03-03 uses
- New NVIDIA GPU C2050
- New physical understanding.
- Nice paper on MD Simulations
- Nightly build version: Parallel IO can not be used with langevin On
- nitrogen in namd
- No. of processors in the namd command.
- nodelist file for concurrent execution of 2 nodes
- NOE
- non-bonded potential in NAMD
- non-zero charge
- NPT equilibration
- NPT simulation schemes
- NPT simulations in NAMD
- Number of MC steps in ABF integrate gives entirely diferent surfaces
- NVE crash
- nvidia 275.09.07 driver
- nvidia cuda driver version
- NVT setup for monolayer
- O-PHOSPHOTYROSINE link to DNA base pair.
- Oh dear, 'namd2 invoked oom-killer' ...
- online guide for using amber ff in NAMD
- OpenCL and AMD GPUs
- OPENING EXTENDED SYSTEM TRAJECTORY FILE
- OPLS mixing rules
- output forces with tclBC
- Output of forces
- Pair interaction and thermo integration
- Pair interaction calculation - Direction of the force
- pair interaction calculations
- pair interaction energy for 2 water molecules
- pair interaction of water molecules
- pair interaction self in 2.7b3
- pairinteractions
- pairinteractionself in 2.7b3
- paper/articule on colvars module
- par_all36_cgenff.prm with NAMD2.7 - problem of file reading
- Parallel replicas?
- parallel scaling issues
- Parallel Simulations
- Parameter File
- parameter file for carbon nanotube
- parameter file for CHARMM
- parameter file for DMPC lipid and protein system but with CHARMM36 lipids
- Parameter file problem
- parameter for TFA (trifluoroacetic acid)
- parameter format for REMD simulations
- Parameter in configuration NVE or NPT
- parameters for Glutathione and BSO
- parameters for graphene nanoribbons annealed by hydrogen
- Parameters/topology entries for non-standard nucleotides
- Paratool`s error reading single point calculation.
- Parse Fep plugin error
- partial charges for organic ligands
- Particle Mesh Ewald question (from the tutorial)
- Patch at AutoPsfBuilder
- patch becoming too small
- patch for phosphotyrosine residue
- Patch link
- patch missing residues
- patch needed for tuple is missing
- PBB File Format/Setup for PBC
- PBC
- PBC Wrap + TMD
- pbc wrap option for x,y,z lengths
- pentacoordinate heme
- Peptide planarity Dihedral angle restraints
- peptide structure
- Performance peoblem about NAMD-CUDA benchmarks
- Periodic Boundary Condition for a 630 Amino Acid Protein
- Periodic Boundary Condition in NAMD
- Periodic Boundary conditions
- periodic boundary conditions in namd energy calculation
- Periodic cell has become too small for original patch grid!
- Periodic cell has become too small for original patch grid!â€
- PhD position in Computational Structural Biology at MPI Muenster
- Phi MD
- phosphate parameters
- phosphorilated serine
- phosphotyrosine
- Pico scale to nanoscale simulation....alteration if .conf files required
- plotting potential energy
- Plumed and NAMD
- PLUMED release 1.2.0 available
- PLUMED release 1.3 available
- PLUMED tutorial announcement
- PME and net charge in the system
- PME for electrostatics and cutoff for vdW?
- PME Grid Settings and its significance relative to a cutoff value
- PME Kappa and Non-bonded Cutoff
- PME or not PME? What happens if PME is turned off?
- PMF
- PMF calculation
- POPC membrane model in pH 4
- Positional restraints - Dielectric constant
- positive total energy
- Possibility of modifying the non-bonded terms of the potential
- possible bug with NAMD Energy plugin
- Possible way of performing a temperature gradient??
- Postdoc Position available
- potential functions in NAMD
- Predicting the binding affinity and anion
- Pressure Calculation
- Pressure is not constant in NPT ensemble
- Pressure parameter in minimization
- Pressure Problems, Excessively High Readings
- Pressure profile calculation problem
- Pressure Questions
- print center of mass
- prm and top files for charmm19 force field
- problem at applying patch
- problem at maintaining geometry coordinate
- Problem building NAMD (multiple definitions)
- problem caused by cluster?
- Problem compiling namd
- Problem Compiling NAMD (version 2.7b2)
- Problem facing during Solvation of Coarse Grain Model
- problem for simulation of membrane protein system
- problem in cgsolvate.tcl while adding CG water to the system
- problem in distance.tcl
- Problem in energy minimization using Fixatoms or Constraints
- problem in generating psf file
- Problem in minimization, Energy "-1.#IND" and bad dcd file.
- problem in restarting
- Problem of compiling Version Nightly Build (2010-02-16)
- Problem of running NAMD
- problem on pair interaction
- Problem on periodic boundary condition
- problem regarding charmm parameter file of carbon nano tube
- problem regarding rattle algorithm
- Problem when using psfgen
- Problem while using MARTINI force field with NAMD 2.8
- problem whit comand "COM"
- problem with cuda version
- Problem with extraBonds
- problem with MD
- Problem with NAMD 2.8 (but not in 2.7) : Endless loop repeating "The last position output ..."
- Problem with NAMD2.8 & prmtop files made with AMBER11/AmberTools1.5
- problem with NVT using TIP4P
- Problem with SPC/E water simulation
- Problem with Targeted molecular dynamics
- Problem with topology file
- problem with water
- problem wuth solvate plugin
- Problems about FEP simulation
- Problems Bionanotechnology Tutorial
- Problems compiling NAMD on 8-core Mac
- Problems installing NAMD
- Problems with AutoPSF
- problems with NAMD plot and .DCD file
- Problems with tcl scripts for REMD simulation
- problems with temperature control
- Proline hybrid topology file for FEP
- Proposed Feature in Targeted MD
- Protein distort during equilibration
- protein fixed in simulation
- Protein in a Lipid Membrane
- protein moving out during npt equilibration
- Protein moving out of box during npt simulation
- protein on solid surface
- protein shifts out of water box
- protein unfolding
- protein unfolding no increase in conf energy
- Protein-DNA simulations
- Protonation
- PSF and PDB file for SWM4 water models
- psf creating for carbon nanotube
- psf file error
- psf of insulin
- psf problem
- psfgen - ACE cap on PRO
- psfgen - any version capable of reading extended PSF files?
- psfgen creates too many bonds in a distorted Fe4S4 cluster
- psfgen error
- psfgen errors
- Psfgen Errors for C-type Heme
- psfgen gives wrong psf file
- psfgen problem, not generating angles/dihedrals
- Q=AD=94=E5=A4=8D:_=E7=AD=94=E5=A4=8D:__compilation_of_n?= amd
- Q=AD=94=E5=A4=8D:__compilation_of_namd?=
- q=AD=94=E5=A4=8D=3A_namd-l=3A_compilation_of?= namd
- Q=B4=D7=D4crazylyf@163.com=B5=C4=D3=CA=BC=FE?=
- Q=B4=D7=D4y=5Fja@163.com=B5=C4=D3=CA=BC=FE?=
- QM/MM
- Quartz modelling
- Query about switch function using AMBER ff99SB forcefield and NAMD simulation code
- Query regarding ABF Tutorial on Methane Hydration
- question about Distance XY
- Question about end of log file
- Question about equilibration
- question about force information
- question about NAMD
- question about namd simulation on protein in tip4p water box
- question about repeating output text
- question about rotation force in SMD
- Question about silver nanoparticle simulation
- Question about Tcl/customising the colvar module
- question about v2.8
- question about wrap atoms to its original coordinates
- Question for Developers: NAMD 2.7 performance issues and Questions about Compiling
- question from a tutorial
- question on hydrogen bond
- question on modifyAppliedForces()
- question on residue rmsd.tcl
- question on the center of mass calculation in colvar
- Question regarding NAMD membrane tutorial
- question regarding warning.
- Questions
- questions about ABF simulations
- questions about Constant Pressure Control (variable volume)
- Questions about lattice information in NAMD2.7b2
- questions about smd
- questions about the heat diffusion calculation in the tutorial
- Questions about thermodynamic integration in NAMD 2.7b2
- questions about user defined potential in NAMD
- Quick TCl scripting question
- Radius of gyration
- ramd firstRamdAtom
- RAMD patch in NAMD CVS
- RAMD scripts and tcl version
- RAMD scripts version 4.1
- RAMD Setting parameter TclForces from script failed
- RBCG
- RBCG electrostatic term
- RBCG water
- RBCG water simulation
- RBCG-dcd files
- RDF.tcl selections
- Re : AW: save the last frame as a pdb file using dcd file
- Re : Setting up a membrane simulation
- re a problem with "Charging a spherical ion"
- Re PMF
- reading dcd file
- Reading files for multiple threaded simulations
- Reading NAMD coor files in CHARMM -> Fail for 64Bit
- reading prameter file
- Reason of FATAL ERROR: UNABLE TO FIND ANGLE PARAMETERS FOR HT HT OT
- reassignFreq expression and relation with SMD
- ReassignFreq script fail!!
- Recent Geforce Cuda GPU cards(GT 440, GTX 560ti)
- Recover high precision coordinates from binary .coor file
- Reduce the frequency of load balancer output
- refphrasing of the question for equilibration script
- reg_membrane_peptide_interaction
- Regarding ligand forcefield
- Regarding NAMD algorithm
- regarding parameter and topology files for a new molecule
- Regarding Periodic Boundary
- Regarding temperature accelerated MD
- REGARDING Topology file
- regarding vmd
- Regenerating a .dcd file
- reinitvels vs restart.vel
- Relationship between High temperature and the boiling point of water
- Relative RMSD constraint
- Relaxed dihedral scans (or how to constrain a dihedral angle to a changing value).
- Release of R.E.D. Server 2.0
- release of RAMD scripts for NAMD 2.6 and 2.7
- Release of the R.E.D.-III.4 tools
- reloadCharges command
- REMD across gpus
- REMD exchange ratios
- REMD segmentation fault
- REMD with IBM SP6 LoadLeveler
- remove translation of protein under spherical boundary conditions
- Removing some water from a .dcd file or .coor file
- Replica Exchange
- Replica exchange MD with NAMD with SGE....
- Replica Exchange Simulations on Blue Gene/P
- replica exchange trans cis isomerisme
- Reply: couldn´t find rsh program
- request help- namd error abortion stack error
- requirements for running the precompiled Linux-x86_64-ibverbs
- rescaling and reassignment parameter
- rescaling velocity
- Resend - ERROR: Atoms moving too fast;
- residue based CG method
- residue based coarse-grained simulation
- Resources for trying out NVIDIA GPUs for free with NAMD
- restart a simulation
- restart ABF
- Restart from anywhere in DCD trajectory
- restart from different snap shots
- Restart MD from a certain point?
- restart problem
- Restart RMSD increase
- Restart simulation
- restart simulation writing in the same .dcd file.
- restart with constraints causes RMSD "jump"
- Restart, discontinuity of energy
- Restart, RMSD increase
- Restarting A NAMD job with velocity file
- restarting a simulation ?
- Restarting an alchemic FEP calculation
- Restarting MD (Disabling Checklist)
- Restarting protein system simulation using different ligand
- restarting simulation
- restraining groups of atoms
- restraining residues in NAMD
- Restraint on XY Plane
- restraint potential used in the ABF calculations
- restraint with colvars mocule
- RetinalTop
- Reverse Mapping of RBCG Model
- Re£º Can DCD trajectory files contain only protein but water surround
- RHDO lattice as a PBC unit Cell in NAMD
- rigid body
- rigid bonds
- rigid molecule
- rmsd
- RMSD Question
- RMSD trajectory
- RNA simulation
- Rotate two linked proteins against each other and calculate energy profile
- rotation question
- rotational restrains
- rough edges of energy landscape when running ABF
- rsh not working
- rule of thumb for dcd sampling frequency?
- run multiple walkers
- run NAMD_2.7B2
- Run simulation in NAMD using files generated by CHARMM-GUI
- run tests with CUDA
- Run-time system modification
- Running AMBER FF with NAMD 2.8-CUDA
- Running bias exchange metadynamics simulations with NAMD
- Running NAMD CUDA
- running namd faster
- Running namd on Apple's XGrid
- Running namd on Mac OS
- Running namd on multiple win32 nodes
- Running NAMD on SGI Altix system
- Running NAMD parallel on two machines with 3 CUDAs
- Running problem with NAMD2.7b
- Running REMD with CHARMM f.f.
- running tcl scripting
- salt bridge
- Sampling schemes with FEP
- SASA of PBD files
- save the last frame as a pdb file using dcd file
- save trajectory only for two residues
- saving psf
- Scaled forces, colvars and harmonic con/restraints
- scaling
- script for calculation of an rmsd
- script for energy minimization of a .dcd file
- script for equilibration
- script for lipid density
- script for targeted molecular dynamics
- Script Help
- scripting error
- scripting problem
- segmentation fault with AMBER topology (cvs code 03.03.2010)
- Segmentation Faults on Mac OS X Lion
- segmentation faults with AMBER topology
- Segmentation violation with adaptive tempering.
- selecting potential binding cavities with MD
- Selection of alchElecLambdaStart
- selection of cholesterol molecules
- selective rigidbonds
- set dummyAtom position changing
- Setting integrator parameters for ABF
- Setting PME Grid Size
- setting transfer rate in IMD protocol
- Setting Up A Langevin Buffer Region
- Setting up a membrane simulation
- Setting up aMD simulation of a membrane protein
- Setting up values in distance colvar
- SHAKE convergence property for CUDA and nonCUDA NAMD
- simulated annealing protocol
- simulating Acetylated lysine substrate complex
- simulating dna
- simulating DNA using namd::
- Simulating more than 20 Million atom system
- simulating TIP4P with NAMD 2.7b2
- simulation box
- simulation cell enlarging too much after restart
- Simulation configuration file not accesible
- simulation error
- Simulation question
- simulation time instead of frames
- Simulations with NAMD
- Simultaneous FEP simulation of two distinct residues
- Size of Timestep
- Slab Boundary Conditions.
- slow heating md
- SMD
- SMD and langevin dynamics
- SMD constant velocity pulling
- SMD for two steered directions
- SMD negative forces
- SMD normal vector
- SMD of three atom at a time
- SMD simulation: stop applying force during simulation?
- SMD-extension
- sodium ion in water
- software/algorithm to cluster protein conformations
- solute movement in periodic box
- Solute moves outside of solvent box
- Solvation in VMD using Non Standard Solvent System
- SOLVED: Failure to run namd-cuda with gtx-470
- some questions about smd
- something is wrong with my equilibration
- specific heat - instability
- specific site-ion LJ parameters and CHARMM general force field
- specify acceptance ratio in REMD
- Specifying Values for Rotating Constraints
- standard state correction of delta G from a PMF
- starting a job
- starting namd
- Steered dynamics
- StepsPerCycle
- Sticking TIP4P water molecules AMBER
- stochastical boundary conditions in NAMD
- Strange (very large) atom motions
- Strange behavior of NAMD 2.7b1
- Strange vdw_dU/dl values in thermodynamic integration
- Stray PME grid charges detected possible bug 2.7b2
- stream files and paratool
- STRIDE Structure Assignment and Ramachandran Plot Beta Strand allowed regions
- structure breaking
- structure of an equilibration script
- subscribe namd-l
- subtlety with PSFGEN - angle/dihedral regeneration
- sucrose top/par
- Sudden crash - any clue about the cause? --> wc[0] status 12 wc[i].opcode 0
- suitable motherboards for both graphical visualization and NAMD-CUDA computation?
- Suspend NAMD (to RAM)
- SV: restart simulation writing in the same .dcd file.
- switching function
- Switching function for cut-off method
- switching function for electrostaic interaction
- SWM4 water model simulation
- SWM4-NDP Simulation
- Symmetry in NAMD, how to achieve during a MD simulation?
- system density
- System net charge
- tabulatd potentials
- targeted molecular dynamics
- TCBG "Hands-on" Workshop on Computational Biophysics, July 12-16, 2010, at San Diego
- tcl forces and tcl 8.5
- Tcl Forces error
- Tcl issue with config script
- tcl script for saving .coor of each frame from dcd file
- Tcl script in NAMD
- TClforce
- tclforces and extrabonds
- tclforces- tcl extension written in c and built with swig
- tclforces: measure distances in NAMD 2.6b2 ?
- Technique issue with free energy calculation on GPU
- Temperature bath
- Temperature during membrane equilibration
- Temperature gradient!
- temperature range for residue-based CG
- temperature-TS with NAMDplot
- tesla 2050 benchmark
- Tetramer protein complex
- The accuracy of FEP calculation
- The biggest system simulated on one TESLA C2050 ?
- the maximum numbers of atoms in NAMD?
- the meaning and effect of reassignFreq and reassignTemp
- the meaning of " 5-ZEROS" " 9-ZEROS" in the DCD file
- the meaning of reassignFreq and reassignTemp
- The Nudged Elastic Band Approach to Find the Lowest Energy Pathway Between two States
- The outputs of REMD were suspended
- The problem of annihilating the solute in the aqueous
- the problem with NAMD2.7b
- the storage format of the coordinate binary file in NAMD
- the total energy of single H2O molecule
- the unit of dipole moment in the calculation of dielectric constant.
- the usage of ++nodelist and ++local
- Thermodynamic integration questions
- time step and total simulation time in conf file
- Timeout waiting for node-program to connect
- Timestep 594
- timing variation during 256core run on abe.ncsa.uiuc.edu
- TIP4P water in AMBER parm7 format fails with 2010-06-07 nightly build
- TIP4P water model
- TIP4P with NPT
- TIP4P/Ice usage in NAMD
- TIP5P water simulation
- TIP5P-model
- TMD and binary coordinate files
- tmd log file
- TMD SCRIPT
- TMD simulations
- top file for CNT
- topology and parameter files
- topology file for dissacharides with psfgen
- Topology file for ethanol
- topology file for nanotube
- topology file for nucleic acids including ammonium ion
- Topology files
- topology for DNA
- topology for monophosphate
- TopoTools for tpr file
- total charge correction
- trajectory in temperature from Replica Exchange MD
- trajectory_path.tcl
- Transferring environment variables when using charmrun
- trouble in dynamics
- trouble running metalloprotein simulation from literature
- Trouble running NAMD on win7
- Trp-cage folding simulation
- Truncated octahedron - unwrapping the trajectory etc
- Truncated octahedron box issues (?)
- Truncated octahedron box issues Q=3F=29?=
- Turning off Electrostatics Completely
- tutorial-l: Nanotubes tutorial - coorList(577) no such element
- two NAMD questions
- Two questions about essential dynamics
- Typo in NAMD 2.8b2 output for Accelerated MD
- Uma wants to chat
- Umbrella sampling
- umbrella sampling by NAMD
- Umbrella Sampling Methodology
- Umbrella sampling-NAMD
- unable to open binary file
- unit of force constant for dihedral angle restrain with extrabonds command
- units of position coordinate velocity coordinate and timestep in .dcd and .veldcd file
- Unpredictable crash at runtime
- Unstable atoms
- unsubcribe
- Unsubscribe
- unsubscribe namd-l
- Update to CUDA error in NAMD 2.7: Increase MAX_EXCLUSIONS: problem persists and CPU-only MD scales poorly
- update: segmentation faults with AMBER topology (cvscode 03 Mar 2010)
- update: segmentation faults with AMBER topology and RAMD tcl scripts
- usage of NAMD with AMBER commands
- Use of RBCG to convert multiple frames from atomistic trajectory to Coarse grained
- user-defined energy function
- Using 'Alignment to principal axes '
- Using ABF to explore the conformational space of a spin label attached to a membrane protein
- Using CHARMM Compatible Amber Parameters
- Using CHARMM-GUI membrane builder with NAMD
- using colvars for bending modulus?
- Using NAMD for Metropolis Monte Carlo conformational searches
- Using RAMD for studiying conformational changes in proteins
- Using RMSD in colvar
- using TIP4P 2005 in namd
- Using VMD paratool
- Various practical colvar module related questions
- VdW and fixatoms
- vdw parameter of metal ion
- VdW parameters for Zn and Fe in metalloproteins
- vdw value in parameter file
- velocities from a DCD file
- Velocity distribution
- velocity error during steered MD
- velocity information
- Version 2.7 problems!
- version of namd to install
- version of tcl in binary builds
- VMD inorganic builder plugin
- vmd-l: Asymmetric water molecule
- vmd-l: CHARMM parameters for Mn 2+ ion
- vmd-l: How to maximize the VMD display window
- vmd-l: measure fit - wrong alignment
- vmd-l: No APBS output: 'cannot access output file' error
- vmd-l: No probability distribution plot in ParseFEP
- vmd-l: Parse Fep plugin error
- vmd-l: ParseFEP output errors
- vmd-l: protein-water RDF
- vmd-l: RMSD Question
- vmd-l: water molecules around proteins
- vmd-l: why atom positions are reset after readpsf, coordpdb commands?
- vmd: ParseFEP plot mistake
- volume calculation
- Volume of the Solution used for MD simulation
- VRPN driver for Novint Falcon haptic device available - Looking for testers
- Warning about PSF file
- Warning: Bad global exclusion count, possible error!
- Warning: DUPLICATE ANGLE ENTRY FOR CPH1-NR1-CPH2 PREVIOUS VALUES
- water "flying out of the box"
- water box deformation
- Water Box Shape Changing during NVT Simulation!
- water content
- water equilibration
- water escape
- water is forming bonds between oxigens
- water sphere
- water sphere plus dielectric
- water structure
- water-molecules/coordenates
- waterbox changes shape during steered molecular dynamics
- Waterbox used in minimization?
- WG: Abnormal EOF Error in Extra Bonds File
- What is the Potential Energy of a Protein in Namdenergy
- What is the proper value of TMDk in TMD simulations?
- what is wrong with this pdb to simulate with NAMD
- what will be the best way to simulate substrate interaction only within a binding pocket of a large protein.
- where can I find parameters for t-BuO(C=O)NH-?
- where do I find info about freeEnergy ?
- Which compiler is used for the official (windows) NAMD binaries
- which one is better to use - fixed atoms or constraints?
- Why are the pressures in my box of water systematically off?
- Why do different versions of NAMD deserve different simulation results?
- Why NAMD run Slow down
- Why NAMD writes colvars step by step
- Win64-MPI
- Windows binaries of NAMD 2.72b supports CUDA?
- WorkDistrib: Recursive bisection fails,invoking least-load algorithm
- Workshop on GPU Programming for Molecular Modeling, August 6-8, 2010, at the Beckman Institute in Urbana, Illinois
- wrapping ions
- wrapping problem
- write out the snapshot from MD trajectory
- writing back coordinates of waters that cross the unit cell
- Wrong energies in CUDA version
- Wrong exit from RAMD runs
- xplor-formated parameters
- Yan: analysis question
- Z-direction shrinking
- Zcoord for ABF
- Zcoord-1atom for ABF
- zeroMomentum for SMD
- zinc-finger protein simulation
- ç”å¤: compilation of namd
Last message date: Sat Dec 31 2011 - 05:23:47 CST
Archived on: Wed Feb 29 2012 - 15:58:02 CST
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