NAMD-L: By Subject
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About this archive
Starting: Mon Jan 02 2012 - 00:44:43 CST
Ending: Tue Dec 31 2013 - 11:28:27 CST
- "Warning" meaning
- 'Hands-On' Workshop on Computational Biophysics using VMD and NAMD, October 22-26, 2012 in Urbana, Illinois
- 'Hands-on' Workshop on Computational Biophysics using VMD, NAMD, and ProDy, June 10-14, 2013 in Pittsburgh, PA
- (no subject)
- .psf file in VMD
- 1-4 tabulated potentials?
- 1-4 vdw scaling?
- 2.9b1 and GPU accelerated GB implicit solvent
- 2.9b1 crashes
- 2014 Aspen Center for Physics Workshop
- 2014 Biophysics Workshop In Aspen Colorado
- 2CPU+1GPU vs 1CPU+2GPU
- 2d periodic box
- 50% system CPU usage when parallel running NAMD on Rocks cluster
- [charm] Charm 6.5.0 compilation issue
- [Checkpoint] BLCR and NAMD
- [MetaD; namd 2.9] Pmf output file problem once the CV boundaries are reached, even using "expandBoundaries on"
- [OT] A new method for quantifying convergence of MD simulations
- [SOLVED] Charmrun> error x attaching to node
- [SUSPICIOUS MESSAGE] Reg System Prepartion namd
- A bug in replica.namd?
- A fancy problem in calculating the protonated glutamic acid modelled by adding the patch of GLUP
- A larger protein data bank for performance benchmark
- a problem about pbc in a namd trajectory
- a question about ensemble
- A question about the CHARMM force field
- a question on version nightly build flatforms
- ABACAVIR parameters
- ABF
- ABF - coordNum collective variable
- ABF - distance between two domains
- ABF calculations in NAMD
- ABF historyFile and distFile
- abf integrate on two dimensional pmf
- ABF simulation
- ABF simulations with barriers (adsorption)
- ABF subdividing the reaction coordinate
- ABF thermostats and energy introduced into the system
- ABF with the RMSD colvar
- ABF zCoord analog in colvars ?
- ABF/Steered MD for DNA Hybridization on Carbon Nanotubes
- ABF: Distances in colvars.traj not identical with VMD exported distances
- abf_integrate
- Abouf Psfgen error
- About "add solvation"
- About a REMD tutorial
- About Bond Deletion
- About Constraint Failure
- about dcd files
- About error during creation of psf file
- About error in .pgn error in vmd cmd prompt
- About Fiorin-Klein-Henin recent colvar examples
- About Free energy tutorial for Membrane-Protein system
- about interaction between protein and its image in namd simulation
- about long namd trajectory and pbc effect
- About Membrane anlysis
- about molecular axis
- About Muticore Linux Ibnstalltion if NAmd
- About NAMD
- About Namd Compilation
- About Namd Installation
- About PLUMED with NAMD VMD
- About psfgen error
- About Psfgen for cyclic peptide
- About Psfgen for membrane
- About restaring Simulation
- About the correction of charging two ion water box by using FEP
- About the scope of show_replicas.vmd
- about trajectory analysis
- About Usage of Topolgy and Parameter
- Accelerated MD
- accelerated MD (aMD) with GPU
- accelerated MD and External Electric Field
- Accelerated MD in NAMD
- Accelerated MD parameters
- accelerated MD parameters for dual boost mode
- AccelMD + GBIS
- accelMD parameter choice
- Accumulating free energy change for applying colvar restraint
- acylated and amidated parameters.
- Adaptive Tempering "OPENING EXTENDED SYSTEM TRAJECTORY FILE" error
- Adaptive tempering exception error
- Adaptive tempering floating point exception
- Add acetyle and amin Group to peptide
- Adding HEME parameters
- Advertisement Workshop Aspen Center for Physics
- Advice on how to perform multiple copy ligand simulation
- Alchemical free-energy methods and electroneutrality
- Alchemical protein transformation with a group of (non proteic) atoms bound to two amino acids
- Alchemical transformations and DDG of point mutations
- Alchemical with parm7 ff
- All CUDA devices are in prohibited mode, of compute capability 1.0, or otherwise unusable.
- Always 24-way SMP?
- Am I doing the Right Thing?
- AMBER in NAMD
- Amber topology
- aMD with implicit solvent - Segmentation fault
- Amorphous Structure code or builder
- an error when merge pdb and psf files in vmd for big model
- Analysis of FEP output file
- analysis of simulation output
- analyzing NAMD trajectory with NAMD Energy
- Annealing of SiO
- Announcement: Large biomolecule benchmark report
- Any alternative to colvars for minimization?
- apoa1 slow Phase 1
- Apply torque with NAMD
- Apply two Different eFeild on the same Direction
- Applying TclBC script every x steps Error
- Approaching Deadline December 1st 2013 - Advanced LAMMPS and Scientific Software Development Workshop at ICTP in March 2014
- Are coordinates in the tclForces module loaded as wrapped?
- Are random forces applied at every step (when using the langevin thermostat) ?
- Aron Broom on NVIDIA CUDA Spotlight
- ask for new toppar files for drude in NAMD2.9
- Asking for Free energy calculation advice
- Aspirin charmm ff
- Assigning atom serial number after the first 99999 atoms
- Assigning Partial Charges to FE in Active Site Superoxide Dismutase.
- Atom indices in collective variable definition
- Atom numbering
- Atomic Radii for GB Implicit Solvent
- Atoms Gone Missing after Generalized Born Implicit Solvent Equilibration
- Atoms moving too fast only with CUDA version.
- Atoms moving too fast with NAMD/Amber
- ATTENTION: 0031-408 4 tasks allocated by LoadLeveler, continuing
- AW:
- AW: "Warning" meaning
- AW: 2CPU+1GPU vs 1CPU+2GPU
- AW: 50% system CPU usage when parallel running NAMD on Rocks cluster
- AW: [SOLVED] Charmrun> error x attaching to node
- AW: A larger protein data bank for performance benchmark
- AW: a problem about pbc in a namd trajectory
- AW: About Bond Deletion
- AW: About Constraint Failure
- AW: about long namd trajectory and pbc effect
- AW: about trajectory analysis
- AW: All CUDA devices are in prohibited mode, of compute capability 1.0, or otherwise unusable.
- AW: Always 24-way SMP?
- AW: Any alternative to colvars for minimization?
- AW: apoa1 slow Phase 1
- AW: Are random forces applied at every step (when using the langevin thermostat) ?
- AW: Assigning Partial Charges to FE in Active Site Superoxide Dismutase.
- AW: Atoms moving too fast only with CUDA version.
- AW: Atoms moving too fast with NAMD/Amber
- AW: AW: 2CPU+1GPU vs 1CPU+2GPU
- AW: AW: Atoms moving too fast only with CUDA version.
- AW: AW: AW: 2CPU+1GPU vs 1CPU+2GPU
- AW: AW: AW: Atoms moving too fast only with CUDA version.
- AW: AW: AW: AW: Atoms moving too fast only with CUDA version.
- AW: AW: AW: AW: Error in membrane protein simulation
- AW: AW: AW: AW: tclBC incorrect output
- AW: AW: AW: CUDA problem?
- AW: AW: AW: Error in membrane protein simulation
- AW: AW: AW: libcudart.so.4 error
- AW: AW: AW: Martini RBCG simulation frequently crashing with "atoms moving too fast"
- AW: AW: AW: NAMD feature request Hydrogenscale
- AW: AW: AW: pbc error
- AW: AW: AW: Running NAMD on Forge (CUDA)
- AW: AW: AW: Sudden energy drop after minimization
- AW: AW: AW: tclBC incorrect output
- AW: AW: center of mass movement removal throughout simulation?
- AW: AW: charm++ MPI build errors on LSF Cluster: "Can not compile a MPI program"
- AW: AW: Coarse-Grained fatal error!
- AW: AW: compress PSF into INTER
- AW: AW: conf file question
- AW: AW: Consistent temperature increase in CUDA runs
- AW: AW: CUDA problem?
- AW: AW: Energy minimization of membrane
- AW: AW: Error in membrane protein simulation
- AW: AW: Generating force field for novel molecules
- AW: AW: hi every body,
- AW: AW: libcudart.so.4 error
- AW: AW: Low CPU usage with NAMD running on linux cluster
- AW: AW: Martini RBCG simulation frequently crashing with "atoms moving too fast"
- AW: AW: Minimisation of protein in a water box
- AW: AW: namd 2.9 ibverbs issues
- AW: AW: namd 2.9 not going so well
- AW: AW: namd 2.9 run instability (segfaults)
- AW: AW: NAMD feature request Hydrogenscale
- AW: AW: No output after "scheduler running in netpoll mode"
- AW: AW: Only one process running on cluster
- AW: AW: problem with pdb psf files!
- AW: AW: Running NAMD on Forge (CUDA)
- AW: AW: Set up NPT simulation in cubic PBC-box
- AW: AW: simulation:protein,ligand,lipid,water and ions
- AW: AW: Simultaneous calculation on CPU-only nodes and CPU/GPU node (with or without rCUDA)
- AW: AW: smd simulation
- AW: AW: Sudden energy drop after minimization
- AW: AW: tclBC incorrect output
- AW: AW: vmd-l: Occupancy maps
- AW: Benchmarks for GTX 690's and 590's
- AW: Bond Breaking in Polymer Networks - United Atom Forcefield
- AW: box dimension for unwrapped boxes?
- AW: BUG: TCL coorfile command
- AW: Build polymer from monomer
- AW: Building crystal polymer
- AW: Bulk properties of polymers
- AW: C++ API
- AW: Can I define a simulation box but turn off the PBC at the same time?
- AW: Can protein-water electrostatic interaction be turned off keeping protein-protein (vdw+elect) and water-water (vdw+elect) interactions intact?
- AW: Can protein-water interaction be turned off keeping protein-protein and water-water interactions intact?
- AW: catdcd error
- AW: catdcd output and .psf file atom count mismatch
- AW: cell origin problem
- AW: center of mass movement removal throughout simulation?
- AW: charm++ MPI build errors on LSF Cluster: "Can not compile a MPI program"
- AW: charm-gui membrane builder
- AW: Coarse-Grained fatal error!
- AW: Coarse-grained reverse transformation
- AW: Colvar cannot be ran on supercomputer newton
- AW: compilation with CUDA error
- AW: compiling charm++ Error: can not find mpi library
- AW: compress PSF into INTER
- AW: conf file question
- AW: Consistent temperature increase in CUDA runs
- AW: converting dcd files to netcdf or ascii
- AW: Coordinate vs. time plots
- AW: Coordinates of Carbon atoms on Graphite
- AW: crossing the border by protein/ion complex
- AW: CUDA error on Pe 4: device cannot map host memory
- AW: Cuda errors in Ubuntu12amd64
- AW: CUDA problem?
- AW: cuda_check_local_progress polled 1000000 times
- AW: DCD writing error on cluster
- AW: DNA surrounded by a shell of water in a big box with vacuum
- AW: Does MOLLY really retain bond motion for water?
- AW: Drifting water molecules
- AW: efield energies incorrect in analysis mode (run 0) ?
- AW: energy minimization
- AW: Energy minimization of membrane
- AW: Error
- AW: Error in distributing the cores for a single processor
- AW: Error in membrane protein simulation
- AW: ERROR: Constraint failure in RATTLE algorithm for atom 593!
- AW: execute vs. config directory
- AW: explicit NVT simulation
- AW: Exploding vdW energies in automatically generated POPC membranes
- AW: Extract KE, PE and total energy from log file
- AW: extract velocities
- AW: FATAL ERROR: CUDA error in cudaGetDeviceCount on Pe 0 (thomasASUS): CUDA driver version is insufficient for CUDA runtime version
- AW: FEP - Dynamic charges
- AW: FEP on an amino acid ligand
- AW: ffTK in the just released VMD 1.9.1
- AW: First meeting with NAMD
- AW: Fixed and SMD atoms
- AW: fixed atom/Constraint failure in RATTLE algorithm/
- AW: fixed bond length
- AW: Fixing bonds in dihydrogen phosphate to save computation time
- AW: floating point reproduceability
- AW: Force Field Topology and Parameter Files
- AW: Fwd: Fwd: namd on gtx-680
- AW: Generating force field for novel molecules
- AW: Glycosaminoglycan sulfate group with CHARMM
- AW: GPU cluster
- AW: GPU workstation build
- AW: GPUs silently stop working during simulation when oversubscribed
- AW: GTX-660 Ti benchmark
- AW: H-bonds cutoff angle criterian
- AW: H-bonds cutoff angle criterian. .
- AW: Help with "ERROR: Constraint failure in RATTLE algorithm for atom XXXX!"
- AW: hi every body,
- AW: How can I write a log file on my cluster?
- AW: how to apply force SMD method on an anisotropic geometry
- AW: how to calculate the box size
- AW: how to do a vacuum minimization without electrostatics and periodic boundary conditions?
- AW: how to edit restart.coor
- AW: How to Get Bonded Pair Force Calculation with NAMD
- AW: how to run NAMD-CUDA on multiple nodes
- AW: IB fabrics
- AW: inconsistency between "Benchmark" and "Timing" output
- AW: increment torsion restrain before minimization
- AW: Installing NAMD on a 64-bit linux (NVIDIA CUDA)
- AW: Keep PBC box size in Z-direction constant?
- AW: keeping a protein in a solvation box
- AW: LES very slow
- AW: libcudart.so.4 error
- AW: Line minimizerfailure because of IMPR?
- AW: Link between simulations
- AW: Linux-x86_64-CUDA version 2.8 on CentOS-5 x86_64 non local user issue?
- AW: Low CPU usage with NAMD running on linux cluster
- AW: making patch
- AW: malloc memory error using CUDA devices
- AW: Martini RBCG simulation frequently crashing with "atoms moving too fast"
- AW: MD crashes at 300K after warm up MD
- AW: memory-optimized version binary coordinates?
- AW: Minimisation of protein in a water box
- AW: minimization and water bubbles
- AW: Multi core problem
- AW: multicore versus net-linux
- AW: Multiple gpu cards
- AW: Mysterious slow down in parallel
- AW: NAMD 2.8 and PLUMED 1.3
- AW: NAMD 2.9 CUDA compilation
- AW: namd 2.9 ibverbs issues
- AW: NAMD 2.9 install on CLuster mpirun/charmrun with ibverb version ?
- AW: namd 2.9 not going so well
- AW: namd 2.9 run instability (segfaults)
- AW: namd 2.9 tip4p-2005
- AW: NAMD 2.9 Windows CUDA build?
- AW: NAMD 2.9 with CUDA runs
- AW: NAMD 2.9: Segmentation fault?
- AW: NAMD 2.9b1 crashes during minimization
- AW: NAMD 2.9b2-cuda does not scale well compared to NAMD 2.8
- AW: NAMD CUDA performance
- AW: NAMD failed to read AMBER parm file
- AW: NAMD feature request Hydrogenscale
- AW: Namd list: "Size cell" for restart
- AW: NAMD PERFORMANCE ON NVIDIA K20 GPU
- AW: NAMD related
- AW: namd scale-up
- AW: NAMD SGE Job Script Scale Up issues!
- AW: namd simulation:protein,ligand,lipid,water and ions
- AW: namd simulation:protein,ligand,lipid,water and ions
- AW: NAMD with Intel Xeon Phi coprocessors ?
- AW: NAMD/VMD installation on Linux Clusters with InfiniBand
- AW: NAMD2.9 single-node benchmarks, 0-2 Kepler GPU's.
- AW: NAMD_2.9_Linux-x86_64-ibverbs RUNS on QueenBee RUN TIME VARIATION
- AW: NAMDenergy plugin_van der Waal interactions
- AW: NAMDEnergy: run with XSC file or not?
- AW: NamdMemoryReduction - genCompressedPsf
- AW: NBFIX 1-4 scaling term ignored for CHARMM format parameters
- AW: Newbie's question
- AW: No output after "scheduler running in netpoll mode"
- AW: no. of CPUs for optimal GTX-690 performance
- AW: Nvidia GPUs
- AW: Only one process running on cluster
- AW: outputting atom coordinated
- AW: parallel code in tclforce script
- AW: Pass a runtime parameter into the configuration file
- AW: pbc error
- AW: PDB sugar unit residue name
- AW: peculiar scaling on the GPU
- AW: Percentage of Residues in Ramachandran Plot regions versus time of trajectory
- AW: performance variation during run time
- AW: periodic boundaries
- AW: periodicity error
- AW: Please read: fatal error namd 2.7b1 for Win32 Memory allocation failed on processor > 0
- AW: problem in solvating a graphene layer created using VMD-nanotube builder
- AW: Problem running NAMD 2.8 with ibverbs
- AW: problem with gpu namd 2.9b3
- AW: Problem with parameter file in Pair Interaction Calculation
- AW: problem with paramters?
- AW: problem with pdb psf files!
- AW: problem with ptch ...
- AW: Problem with replica exchange
- AW: problem with runiing namd through infiniband
- AW: Protein unfolding and Coarse grained
- AW: puzzle of SMD in NAMD-2.9 and pull code in Gromacs
- AW: queries about "Tclforces" utility in NAMD
- AW: Question about GPUs hardware.
- AW: Question about how much used from CPU?
- AW: Question about loading velocity files on VMD
- AW: question and NAMD operation
- AW: question regarding simulated annealing
- AW: questions regarding the source code in NAMD
- AW: Random seed and equilibrated structure
- AW: RATTLE algorithm
- AW: rcmd: socket: All ports in use w/ NAMD_2.9_Linux-x86_64-ibverbs
- AW: Reflecting boundary z axis in NAMD
- AW: Regarding installing Namd 2.9 on windows xp 32 bit system
- AW: remd run command question
- AW: Replica exchange, colvars & harmonic restraints
- AW: Replica-exchange MD on a single node / SMP workstation
- AW: residue_rmsd.tcl via
- AW: restart a simulation
- AW: Restart simulation of an equilibrated bilayer with sugar molecules inserted
- AW: restraining
- AW: Runaway cuda-enabled namd2 processes
- AW: running namd in parallel
- AW: running NAMD on Amazon EC2?
- AW: Running NAMD on Forge (CUDA)
- AW: Running namd on linux in cpu+gpu mode
- AW: Running NAMD on SGE cluster - multiple modes and cores
- AW: scaling
- AW: Scaling on 64 core nodes?
- AW: Scaling problem: 4 nodes OK, 5 fails to start
- AW: scnb value to prevent VDWs scaling
- AW: secondary structure analysis
- AW: segmentation fault with NAMDenergy
- AW: Separate water coordinates from graphite
- AW: Set up NPT simulation in cubic PBC-box
- AW: SHAKE Tolerance and Performance
- AW: Simulation Box Deformation
- AW: simulation:protein,ligand,lipid,water and ions
- AW: Simultaneous calculation on CPU-only nodes and CPU/GPU node (with or without rCUDA)
- AW: smd simulation
- AW: solvated system for minimization
- AW: spectrum simulation
- AW: stereo-chemical inversion during MD
- AW: Sudden energy drop after minimization
- AW: Suggestions while building a GPU-machine (CUDA) for NAMD use!
- AW: system splitted
- AW: tclBC incorrect output
- AW: TclForces and efficient PBC corrections
- AW: The size of a periodic cell in NAMD operation
- AW: The structure files for the second turn of simulation
- AW: Three GPU cards on shared-mem motherboard
- AW: Trouble loading frames from large DCD files
- AW: Trying to run a setup with amber force field in NAMD
- AW: Two GPU-based workstation
- AW: Unexplained segmentation faults in NAMD 2.9 using CUDA and GBIS
- AW: VDW energy is negative but total energy is positive
- AW: vmd-l: AMD vs. nvidia support
- AW: vmd-l: Creating custom molecule in VMD scripting
- AW: vmd-l: Error: Maximum number of bonds exceeded
- AW: vmd-l: fftk-charges
- AW: vmd-l: Finding particles that are close
- AW: vmd-l: how to enable multiple core rendering?
- AW: vmd-l: matching part of two models
- AW: vmd-l: non-orthorhombic PBCs
- AW: vmd-l: Occupancy maps
- AW: vmd-l: SangbaeLee: question about pbc wrap
- AW: vmd-l: segmentation fault with NAMDenergy
- AW: VMD_waterbox
- AW: Warning: Not all atoms have unique coordinates
- AW: Water bubbles in NVT equilibration dynamics
- AW: water molecules
- AW: what restraint can I use to prevent membrane diffusion on the Z-axis?
- AW: Why does my volume suddenly expand as I increase temperature.
- AW: wrap dcd files
- AW: writedcd problem
- AW: Writing an output file into pdb format in a simulation.
- AW: 回复: Shift (or offset) of the lipid bilayer along Z axis during equilibration
- Bad global bond count
- BAR-estimator error of ParseFEP plugin version 1.5 in VMD 1.9.1
- Basic question about impropers
- Basic question on fixed atom
- Behavior of explicit water beyond periodic boundaries
- Benchmarks for GTX 690's and 590's
- Benefits of SandyBridge EP in NAMD2.9
- bilayer creation
- binding free energy calculation
- Biotin force field
- BKS potential
- BLCR and NAMD
- Bond Breaking in Polymer Networks - United Atom Forcefield
- Bonds in XPLOR format
- box dimension for unwrapped boxes?
- Breaking of Disulfide Bonds
- Buffer Underflow in Multiple Walker MetaDynamics
- Bug in SASA for alanin example
- Bug in T-REMD with colvars
- BUG Report: NAMD 2.10 Nightly Build from 11.Sep
- Bug with BOUNDARY energy in postprocessing?
- bugs in NAMD_TI script?
- Build polymer from monomer
- Building crystal polymer
- Bulk properties of polymers
- C++ API
- Calculate binding free energy
- Calculating Potential Energy for an atom selection
- Calculating pressure on each direction
- Can a small langevinDamping coefficient lead to 'ERROR: atoms moving too fast'?
- Can I define a simulation box but turn off the PBC at the same time?
- can i use swap partition to increase ram in namd?
- Can protein-water electrostatic interaction be turned off keeping protein-protein (vdw+elect) and water-water (vdw+elect) interactions intact?
- Can protein-water interaction be turned off keeping protein-protein and water-water interactions intact?
- can TMD alignment prior to force calculation be turned off?
- can't run multiple jobs with multiple gpus
- Carma v.1.2 released.
- Carma v.1.3 available for download
- catdcd error
- catdcd output and .psf file atom count mismatch
- CatDCD windows binaries
- cell origin problem
- cell shape after increasing margin (parm7 ff)
- Cellulose MD simulations
- center of mass calculation in the tcl interface
- Center of mass motion included in Temperature?
- center of mass movement removal throughout simulation?
- CHAMBER generated .prmtop file is not compatable with namd2
- changing harmonic restraints (colvars)
- Changing NAMD XY restraint
- Charge distribution
- charging free energies with alchdecouple
- Charm 6.5.0 compilation issue
- charm++ MPI build errors on LSF Cluster: "Can not compile a MPI program"
- charm-gui membrane builder
- CHARMGUI and ligands parametrisation
- charmm param ... wrong charges
- CHARMM parameters and topology for YO-PRO and/or Lucyfer Yellow
- charmm to namd conversion
- charmm toppar in namd
- CHARMM-c36, glycans and RATTLE
- CHARMM-GUI running error for ligand
- charmrun setup
- checkpoint and revert
- CNT builder
- CNT coarse grain
- Coarse grain parameter files
- Coarse-Grained fatal error!
- Coarse-grained reverse transformation
- colavrs ABF restart not matching
- collective variable component -- eigenvector usage
- Collective variable data analysis using WHAM
- Collective variable on COM instead of COG
- collective variables new paper
- Colvar cannot be ran on supercomputer newton
- colvar keyword ForceNoPBC
- colvars and parallel-tempering with namd2.10
- colvars configuration file example
- Colvars Error?
- Colvars periodic boundary treatment question
- Colvars RMSD syntax with a moving reference frame
- Colvars value is out of boundary
- Combining several proteins of the same type together
- compilation with CUDA error
- Compile NAMD with FFTW3 and MPI
- Compile NAMD2.9 on Xeon Phi
- Compiling and running NAMD on multiple nodes of SDSC Trestles
- compiling charm++ Error: can not find mpi library
- Compiling NAMD
- Compiling NAMD 2.9 on BlueGene/Q
- Compiling NAMD on NICS Kraken
- Compiling NAMD with CUDA on MacOSX Mountain Lion
- compiling namd-2.9 on bluegeneQ
- Compiling NAMD_2.9b2_Source with GCC 4.7.0
- compress PSF into INTER
- Computational Biophysics Workshop using NAMD and VMD, November 18-22, 2013, Urbana, Illinois, USA
- Computational Electrostatics for Biological Application (CEBA'13) - July 1-3 2013 - Genoa - Italy
- Conceptual questions about GPU acceleration
- Concerning Restarting Multiple Walkers MetaDynamics
- conf file question
- confines volume effects
- Conflict between CUDA NAMD and PMEMD
- connect a spring between all the atoms present in pdb structure
- Consistent temperature increase in CUDA runs
- Constant pressure energy minimization
- Constant Pull Velocity
- constant pulling velocity in SMD
- constant velocity of carbon nanotube through water
- Constant volume energy minimization
- Constraint failure in RATTLE algorithm occurs during NAMD simulation with amber force field
- Controlling fans on a GTX 560 ti
- convergence of FEP calculation.
- Convergence of Sampling and Deciding on Simulation Length
- Convergence of the Gram-Charlier expansion
- converting dcd files to netcdf or ascii
- Coordinate vs. time plots
- Coordinates of Carbon atoms on Graphite
- Copper ion moving out of the protein towards bulk solvent
- could acpype output file be used for NAMD CHARMM FF?
- create junction between nanotubes
- creating a protonated cytidine entry
- creating coarse grain model with martini force field
- cross terms
- crossing the border by protein/ion complex
- crossterm error
- CUDA - OwnerBox::close failure
- cuda error
- CUDA error (as a misleding error message)
- CUDA error 0 attaching to node
- CUDA error in cuda_check_remote_progress on Pe 2
- CUDA error memcpy to exclusions: invalid argument
- CUDA error on Pe 4: device cannot map host memory
- CUDA error vs clashes
- Cuda errors in Ubuntu12amd64
- CUDA limitations
- CUDA problem with 2.9b2
- CUDA problem?
- CUDA vd non-CUDA for minimization
- CUDA workstation
- cuda_check_local_progress polled 1000000 times
- Current bias values
- Current CVS broken? (SortedArray.h)
- cylinder constraint with colvar
- DCD
- DCD file doubles a monomer
- dcd to pdb for trajectory analysis
- DCD writing error on cluster
- Defining colvars groups of atoms for ABF
- delta-G calculation
- DEVELOPER QUESTION -> NAMD Internal energy unit and TCL interface
- Dielectric constant for MDFF of a membrane protein.
- different seeds and protein behavior
- diffusion of protein into water box
- dihedral parameter conversion
- direction of pull in namd
- discrepancy in results from different machines!
- Displaying the gradient tolerance in the output
- Displaying the gradient tolerance in the output as the example output from tutorial 1-2 Water Sphere
- Distance Constraints in ABF Simulation
- distanceZ - harmonic restraints
- DNA surrounded by a shell of water in a big box with vacuum
- DNA system and PH control
- DNA terminals and charges
- Does MOLLY really retain bond motion for water?
- Does NAMD read the PDB element field?
- Does stray PME charges with T-REMD mean insufficient resources and can explicit water abandoned for implicit GB?
- Drifting water molecules
- Drude polarizable force field
- Drude polarizable models with namd
- drude water in namd
- drude water simulation bug ?
- drude water simulation bug ? radial distrubuion function
- Drug design issue.
- dump specific atom positions into a txt file during the simulation
- duplicate residue key
- dynamic_cast cannot be done without runtime type information
- editing the code of the non bonded pair potentials
- Effect of phi, psi cross term map (CMAP) correction on result of MD simulation
- efield energies incorrect in analysis mode (run 0) ?
- eigenvector colvar
- Energy Correction Term For PME Electrostatics in a Charged Periodic System
- energy minimization
- Energy minimization of membrane
- Epoxy CHARMM
- equilibrate conf file
- equilibrate glycerol molecules
- Equilibration of the membrane bilayers with CUDA-support
- Equilibration of the membrane-protein system done in CHARMM-GUI
- Erratic pressure values during equilibration of water box
- Error
- Error in distributing the cores for a single processor
- Error in implicit solvent MD
- Error in membrane protein simulation
- Error in NAMD 2.8 function
- error in psf file
- Error in PSF gen
- ERROR IN TIP4P WATER SIMULATION IN NAMD2.9
- error regarding membrane embedded protein
- error when doing minimization with the charmm Drude FF
- Error while running the infiniband version.
- Error with dummy atoms
- Error with NAMD Energy
- Error with show_replicas.vmd
- ERROR: 0031-250 task 0: Terminated
- ERROR: Constraint failure in RATTLE algorithm for atom 474!
- ERROR: Constraint failure in RATTLE algorithm for atom 593!
- ERROR: Could not translate the value....into a Vector for the option 'cellOrigin'
- Error: periodicity of dihedral zero
- Errors compiling namd with CUDA
- Errors compiling namd with CUDA. .
- Evaluate energy of "protein + two closest ions"
- Evaluate Work for Targeted Molecular Dynamics Simulations
- Ewald contribution to pressure profile only working on single core
- excluded interactions (NNB) in psf file for FEP simulations
- execute vs. config directory
- expandBoundaries and multiple walker metadynamics
- experimental density value
- explicit NVT simulation
- Exploding vdW energies in automatically generated POPC membranes
- Extent of Sampling possible using classical all-atom MD Simulations
- External electric field using Grid
- Extract KE, PE and total energy from log file
- extract velocities
- fail to guess missing coordinates
- Failure with compilation namd2.9-cuda_plumed1.3_recon
- FATAL ERROR : Line too long in pdb file
- FATAL ERROR : Line too long in pdb file]
- Fatal Error by charmc.../usr/bin/ld: cannot find -lsrfftw. Please help!
- fatal error running namd on Mac
- FATAL ERROR Unknown parameter in charmm parameter file
- FATAL ERROR: Bad global bond count!
- FATAL ERROR: CUDA error in cudaGetDeviceCount on Pe 0 (thomasASUS): CUDA driver version is insufficient for CUDA runtime version
- FATAL ERROR: DIDN'T FIND vdW PARAMETER FOR ATOM TYPE AUC
- FATAL ERROR: DIDN'T FIND vdW PARAMETER FOR ATOM TYPE CG2R
- Fe-N bond parameters
- FEP - Dynamic charges
- FEP calculations: optimizing the dlambda, number of steps
- FEP difficulties between two ion species
- FEP Error - TCL
- FEP failure - FFTW problem?
- FEP on an amino acid ligand
- FEP OpenMPI Error
- FEP simulation on membrane protein
- FEP simulation using AmberFF
- FEP simulation: protein moving out of water box.
- FEP tutorial-my molecule doesn't show up in VMD
- FEP using amber topologies
- fep/parm7
- FFTK Atom types
- ffTK in the just released VMD 1.9.1
- FFTK VMD plugin issue (arising from VECSCALE TCL issues of either NAMD or VMD ?)
- file for fixed atoms is not found! - but the file exist actually
- Final link of namd2 executable fails under AIX with xlC compiler
- First impressions from AMBER ff12SB ?
- First meeting with NAMD
- five 'ERROR' in the log file of NAMD2.9
- Fixed and SMD atoms
- fixed atom/Constraint failure in RATTLE algorithm/
- Fixed atoms in SMD
- fixed bond length
- Fixing bonds in dihydrogen phosphate to save computation time
- Fixing Langevin piston to allow off-diagonal stress (and why does the source say "FIX THIS"?)
- Flags for TIP3 water with NAMD/AMBER FF
- flipdcd corrupting dcd files
- floating point reproduceability
- Force field parameter and topology for zinc finger protein
- Force Field Parameters for PEG
- force field parameters for Silicon
- Force field Parametrization
- Force Field Topology and Parameter Files
- forces saved in forcedcd
- forward
- Free energy calculation of proton transfer with FEP
- Free Energy Calculation Question
- Free energy calculations
- free energy methods cheat-sheet/comparison chart
- Free Energy using atomic coordinates as CVs
- FullDirect Electrostatics
- Functional form to apply constraints
- Functionalizing the nanopore
- Fwd:
- Fwd: About "add solvation"
- Fwd: AW: stereo-chemical inversion during MD
- Fwd: Bug in T-REMD with colvars
- Fwd: Can protein-water interaction be turned off keeping protein-protein and water-water interactions intact?
- Fwd: charm-gui membrane builder
- Fwd: CUDA error 0 attaching to node
- Fwd: CUDA error in cuda_check_remote_progress on Pe 2
- Fwd: CUDA error vs clashes
- Fwd: deca-alanin folding by remd parallel tempering
- Fwd: Error in PSF gen
- Fwd: Failure with compilation namd2.9-cuda_plumed1.3_recon
- Fwd: Fwd: Fwd: namd on gtx-680
- Fwd: Fwd: namd on gtx-680
- Fwd: GPU workstation build
- Fwd: Inconsistency in fast table energy vs force
- Fwd: Line minimizerfailure because of IMPR?
- Fwd: Low global exclusion count on parallel tempering, not on MD
- Fwd: NAMD + PLUMED COMPILATION
- Fwd: NAMD 2.9 CUDA compilation
- Fwd: namd cuda error.
- Fwd: namd on gtx-680
- Fwd: NAMD tcouple atoms moving too fast
- Fwd: PCIexpress 3.0 for MD with NAMD on GPUs
- Fwd: Pressure in NPT ensamble
- Fwd: replica exchange and colvars
- Fwd: Restarting T-REMD with colvars
- Fwd: SOLVED, however multiple CUDA efficiency?
- Fwd: stereo-chemical inversion during MD
- Fwd: Stray PME grid charges on increasing number of replicas and T-range with T-REMD
- Fwd: Three GPU cards on shared-mem motherboard
- Fwd: Troubles to converge while running bidirectional FEP
- Fwd: vmd-l: HEME acting unplanar
- Fwd: what restraint can I use to prevent membrane diffusion on the Z-axis?
- Galilean Invariant Thermostat
- GBIS and hydrophobic solvation
- GBIS and thermostats
- Generalized Born Solvent Question
- Generating force field for novel molecules
- Generating topology files for crystalline materials
- gentoo ebuild
- Geometric center of a residue over time
- geometry deformation
- get topology and parameter file for the ligand.
- Getting "nan" at ELEC energy value
- Glycosaminoglycan sulfate group with CHARMM
- Go model in NAMD?
- Gold nanoparticle
- GPCR MD Tutorial
- GPU acceleration by using ATI video card
- GPU cluster
- GPU workstation build
- GPUs silently stop working during simulation when oversubscribed
- Graphene pdb/psf files cannot be read by psfgen
- grcarma : a graphical user interface to carma
- Grid Forces: example code, documentation edit, and requested feature
- Gromacs analysis tools for Namd output
- gromacs to NAMD
- GTX-660 Ti benchmark
- gtx-680: CUDA error in cudaGetDeviceCount
- gurukatagi@gmail.com
- H-bonds cutoff angle criterian
- handling buckingham potentials in NAMD - regd
- Handling torsional potentials other than CHARMM type - regd
- Hard sphere potential
- Harmonic Constrain like MMFP in CHARMM
- has system reached a steady state condition?
- hbonds colvar component
- help on building PATCH
- Help regarding PMF with SMD
- Help with "ERROR: Constraint failure in RATTLE algorithm for atom XXXX!"
- help with how pbc are defined.
- help with how pbc are defined.. .
- HEME acting unplanar
- HEME B PARAMETERS
- Hi
- hi every body,
- HMMM model
- Hole
- how can i demonstrate that a chain-like molecule within a membrane.
- How can I write a log file on my cluster?
- how do I pass environmental variables to namd on BlueGene/P?
- how does NAMD calculate intramolecular electrostatic interactions between Drude pairs?
- how does namd handle violations of the minimum image convention?
- How does NAMD treat a bond across periodic boundaries
- How I can to change the force field function in NAMD for protein phi-value analysis
- How Pressureprofile output are averaged ?
- how to apply force SMD method on an anisotropic geometry
- How to apply Symmetry boundary on NAMD
- How to calculate surface tension properly
- how to calculate the box size
- How to compile NAMD2.9 in IBM AIX UNIX$B!)(B
- How to compute "only the GB Energy" using NAMD?
- How to converse Coarse-Grained structure into all-atom structure
- how to convert CHARMM TIP3P to traditional TIP3P
- How to create psf for graphene
- How to decide whether an ABF curve has been converged?
- how to do a vacuum minimization without electrostatics and periodic boundary conditions?
- how to edit restart.coor
- how to find cellorigin for periodic boundary condition
- how to generate psf for membrane+protein
- How to Get Bonded Pair Force Calculation with NAMD
- How to get cell information from within calcforces in TclForces
- How to improve the GPU utility in NAMD
- How to optimize parameters in command for NAMD CUDA GPU MD calculations?
- How to parameterize Protein ligand complex in membrane?
- How to prepare FEP input files for double mutant
- How to recenter a waterbox with ions around my protein?
- How to remove center of mass translation of macromolecule
- How to replace NAMD electrostatics
- How to restraint pairinteractions
- how to run NAMD-CUDA on multiple nodes
- How to set protonation states of certain atom in DNA with namd/vmd
- How to setting tilt component in colvars module
- how to solve such kind of crossterm parameter problem?
- How to split large NAMD DCD file
- how to switch off protein-water electrostatic interaction keeping the protein-water vdw interactions intact
- how to understand vdwForceSwitching
- How to use ParseFEP plugin to carry out FEP analysis for several forward and backward *.fepout files when lambda is from 0 to 1
- How to write dcd file within Tclforce script
- How we can merge protein and ligand complex?
- Hybrid Monte Carlo?
- I have a question about pair interaction energy calculations.
- IB fabrics
- if{} statements
- Implementation of ELASTIC NETWORK model in NAMD
- implicit solvent
- Implicit water with explicit ions
- Importing a DCD into Mathematica
- In-Residence Training at the Theoretical & Computational Biophysics Group, July 16-27, 2012
- incompatibility between NAMD and amber topology files
- inconsistency between "Benchmark" and "Timing" output
- Inconsistency in fast table energy vs force
- Incorporating some ions with specific location
- incorrect bond
- increment torsion restrain before minimization
- Information about error compiling with CUDA
- Input configuration files for GPU version of NAMD
- inputPrefix for ABF
- inputPrefix in ABF
- Insertion of GPCR in the POPC Bilayer
- Instabilities in Minimization
- Installing NAMD on a 64-bit linux (NVIDIA CUDA)
- Interaction energy definition
- intergation algoritm of NAMD
- Internal Unit system
- Invitation to connect on LinkedIn
- ion placement method vs total energy of the system
- is it possible to strip the restrain linearly?
- Is the TMD equation in the user manual correct?
- is zeroMomentum safe in a steered MD simulation?
- issue with solute that splits
- Issues with 'Gyration' in Colvars module
- Issues with the "Keep Water Out" tcl script
- jobs failed
- jobs with Intel i7
- Keep PBC box size in Z-direction constant?
- keeping a protein in a solvation box
- Keeping water out of the binding pocket with ColVar
- laptop GPU support
- Launching namd GPU-MPI vs GPU-binary
- LCPO SASA Calculation on the GPU
- Lenard Jones coefficients for Neon atoms
- Lennard Jones (LJ) parameters
- LES very slow
- libcudart.so.4 error
- Ligand in association with water
- Line minimizerfailure because of IMPR?
- Linear force ramp increments in ABF
- Link between simulations
- Linux-x86_64-CUDA version 2.8 on CentOS-5 x86_64 non local user issue?
- Linuxtag
- Lipid bilayer tears apart during simulation
- LJcorrection
- local pressure profile for water liquid-vapor
- Locally Enhanced Sampling
- lone pair velocities
- lookup tables
- loop-to-helix change during SMD
- Low CPU usage with NAMD running on linux cluster
- Low global exclusion count on parallel tempering, not on MD
- Mac OS Binary for NAMD 2.10
- making force grids
- making patch
- malloc memory error using CUDA devices
- Margin setup
- Martini 2.2 and ElNeDyn in NAMD
- MARTINI Bad global angle count
- martini force field
- Martini parameter files
- Martini RBCG
- Martini RBCG simulation frequently crashing with "atoms moving too fast"
- MD crashes at 300K after warm up MD
- MD- GPU
- MDFF - should hydrogens be included?
- mdff energy calculation
- mdff error
- MDFF for huge trajectories
- MDFF for protein complex
- MDFF force threshold
- MDFF volumetric map
- membrane bilayer crosses the z axis boundaries of the box and separates into two layers
- membrane GPCR-ligands simulations
- membrane protein simulation lipid bilayer question
- Membrane/peptide system. Water moving from one layer to the other ...
- memory demands of REMD
- memory-optimized version binary coordinates?
- merge pdb/psf files by psfgen - sets coordinates to zero
- metadynamics
- Metadynamics and Colvar Width
- MetaDynamics in 2.9b2 Question
- Metadynamics pmf restart
- Metadynamics Problems
- metadynamics/ABF simulations using collective variables - issues with restarting the calculations
- Method for solvation of protein
- Minimisation issue
- Minimisation of protein in a water box
- Minimisation problem
- minimization and water bubbles
- minimization does not converge
- minimization with symmetry restrain
- minimization, slow heating and then Langevin free runs
- Minimization/Equilibrium problem, atoms moving too fast
- minimizer slowly moving atoms with bad contacts downhill
- Missing angle parameters in the ffTK
- MM-PBSA calculation
- MMPBSA calculation using NAMD
- MMPBSA-like analysis
- modeling missing loops in starting structures
- Modify Molecule.C to avoid fatal error?
- Molecular Shape Searching on GPUs
- Morse potentail with charmm 27
- Moving atoms with bad contacts followed by CUDA error
- Multi core problem
- Multi node run causes "CUDA error cudaStreamCreate"
- Multicore executable error
- Multicore executable error with hydrogens
- multicore versus net-linux
- Multiple copy ligand simulations
- multiple dynamic sections in the config file?
- Multiple gpu cards
- multiple vectors in SMD
- My calcforces does not work properly after a unknown point of the simulation.
- Mysterious slow down in parallel
- n-terminus in my psfgen created pdb/psf file is missing
- NAMD "tCouple" option
- NAMD (and VMD) fail to read simple AMBER prmtop file (and it's not the SCEE and SCNB flags)
- NAMD + PLUMED COMPILATION
- NAMD 2.8 and PLUMED 1.3
- namd 2.9 and plumed
- NAMD 2.9 CUDA compilation
- NAMD 2.9 CUDA multicore, single machine
- namd 2.9 ibverbs issues
- NAMD 2.9 ibverbs: Charmrun crashing on checkpoint-restart
- NAMD 2.9 install on CLuster mpirun/charmrun with ibverb version ?
- NAMD 2.9 jobs hanging.
- namd 2.9 not going so well
- NAMD 2.9 not migrating to computing nodes on Windows Server 2008 R2 HPC MPI
- Namd 2.9 on a BlueGene/Q machine
- NAMD 2.9 released
- NAMD 2.9 Replica Exchange (+replicas error)
- namd 2.9 Replica Exchange with colvar
- NAMD 2.9 Replica-exchange. FATAL ERROR: Unknown command-line option +replicas
- namd 2.9 run instability (segfaults)
- namd 2.9 tip4p-2005
- NAMD 2.9 Windows CUDA build?
- NAMD 2.9 with CUDA runs
- NAMD 2.9: Segmentation fault?
- NAMD 2.9b1 crashes during minimization
- NAMD 2.9b1 released
- NAMD 2.9b2 released
- NAMD 2.9b2-cuda does not scale well compared to NAMD 2.8
- NAMD 2.9b2-cuda does not scale well compared to NAMD 2.8 (solved)
- NAMD 2.9b3 colvars oddity
- NAMD 2.9b3 released
- Namd and CUDA on Debian Wheezy
- NAMD and new FF CHARMM36
- NAMD and water models
- namd and x-plor
- NAMD build problems on PowerPC under Red Hat Enterprise
- NAMD compilation -- compiler issue
- namd conf file
- NAMD configuration file
- namd crashes after 300K steps
- NAMD CUDA 2.9 Performance drop compared to 2.8
- namd cuda error.
- NAMD CUDA performance
- NAMD does not exit simulation on satisfying condition in the tclforces script
- NAMD electrostatic interaction Failure
- NAMD electrostatic interaction Failure.
- Namd energy plugin
- NAMD exiting on startup phase
- NAMD failed to read AMBER parm file
- NAMD feature request Hydrogenscale
- NAMD fixes for dummy atoms & parameters for divalent metal ions
- NAMD in parallel on CPUs of different type
- NAMD Internal energy unit
- NAMD job submission on Kraken?
- Namd list: "Size cell" for restart
- Namd list: Problem in equilibration stage
- NAMD mailing list unsubscribe instructions
- NAMD on Bluegene
- namd on nvidia 302.17
- NAMD on Peta-Scale Machines
- NAMD on ranger.tacc
- NAMD on Stampede
- NAMD on Stempede (and other MIC Coprocessor systems)
- Namd options from TCL
- NAMD Output files
- NAMD parameters +mergegrids +ignoresharing
- NAMD PBS Parallel Job Error
- NAMD PERFORMANCE ON NVIDIA K20 GPU
- NAMD post processing analysis....
- NAMD pressureProfile command
- NAMD pulling one domain
- namd question in parameter conversion
- NAMD related
- NAMD Run Instabilities
- namd runs on compute nodes but not update files in the head node
- namd scale-up
- NAMD SGE Job Script Scale Up issues!
- NAMD simulation with flag similar to -maxh in Gromacs
- namd simulation:protein,ligand,lipid,water and ions
- namd simulation:protein,ligand,lipid,water and ions
- NAMD Tutorial - Water Sphere - Altering size of water sphere
- namd with ff99sb
- NAMD with Intel Xeon Phi coprocessors ?
- NAMD with NVIDIA Quadro K5000?
- NAMD with pbs script
- Namd, lammps comparing energies
- NAMD- molecular dynamics
- namd-I: sub-routine code in NAMD
- NAMD-INCONSISTENCY IN SCOR
- namd-l digest V1 #787
- namd-l digest V1 #918
- namd-l digest V1 #949
- namd-l digest V1 #979
- namd/bluegeneQ
- NAMD/VMD installation on Linux Clusters with InfiniBand
- namd/vmd support to GTX-6## series
- namd2 CUDA errors for non-superusers in Debian
- NAMD2.9 Release and Multi-GPU Minimization Errors
- NAMD2.9 single-node benchmarks, 0-2 Kepler GPU's.
- Namd: nohup: ignoring input and redirecting stderr to stdout
- NAMD_2.9_Linux-x86_64-ibverbs RUNS on QueenBee RUN TIME VARIATION
- NAMD_multiprocessor
- namdenergy and namd
- NAMDenergy plugin_van der Waal interactions
- NAMDEnergy: run with XSC file or not?
- NamdMemoryReduction - genCompressedPsf
- NBFIX 1-4 scaling term ignored for CHARMM format parameters
- NBTABLE issue
- need help in using colvars option
- Need help preventing hydration of the lipid-protein interface in my system
- Negative surface area?
- negative VdW energy and Elect energy
- New empirical force field tools: Release of R.E.D. Server Dev./R.E.D. Python
- New: Colvars project page
- Newbie's question
- Nicolas te ha dejado un mensaje...
- no CUDA-capable device is detected
- No output after "scheduler running in netpoll mode"
- no output for corrfunc
- no. of CPUs for optimal GTX-690 performance
- non integer total charge
- non integral charges
- Non-equilibrium effects in ABF runs
- Nonbonded 3-body potential
- Nonstandard ligand-DNA system
- Nonzero BOUNDARY ENERGY without periodic boundary conditions
- Normal Mode Analysis in NAMD
- not fatal error but no more information
- not reading improper angle from amber1.5 ff12SB
- NOTICE: mail delivery status
- NPT at 100 bar
- Nucleic acid-small molecule system
- nucleic acids - total charge
- Nvidia GPUs
- obtaining cellBasisVectors from SCALE entries in the PDB file
- obtaining the system force
- One Chain Simulation
- one question about gtp flipping in namd simulation
- one-sided harmonic restraint potential
- Only one process running on cluster
- openAtom/NAMD2.9 implementation
- OpenMPI FEP Yields SegFaults and/or infinite dG
- optimal CPU number for parallel MD of a small system
- Organic molecule and membrane. NAMD gives fatal error:
- Orientation colvar + metadynamics questions
- Oscillating Electric Field
- output nonbonded and bonded terms separately
- Output of thermodynamic integration
- outputting atom coordinated
- Overestimated PMF
- pair interaction energy calculation
- pairInteraction and PME
- pairInteractionSelf interaction terms
- pairlist violations
- parallel code in tclforce script
- Parametarization and geometry optimization
- Parametarization and geometry optimization. .
- Parameter file for DGEBA
- parameter file for POPC (RBCG model)
- Parameters for 3 methyl histidine.
- Parameters for Cesium
- Parameters for prosthetic groups
- Pass a runtime parameter into the configuration file
- Patch information for 1TUB.pdb in order to use "psfgen"
- Patching N- and C-Terms and their parameters
- Patching protein with phosphoserine, phosphothreonine and phosphotyrosine patches
- pbc error
- pbc precision
- pbc problem
- pbc wrap
- PCIexpress 3.0 for MD with NAMD on GPUs
- PDB sugar unit residue name
- peculiar scaling on the GPU
- Peptide insertion into a membrane
- Percentage of Residues in Ramachandran Plot regions versus time of trajectory
- performance loss on GPUs
- performance variation during run time
- periodic boundaries
- Periodic cell has become too small
- periodicity error
- pH calculation
- Phosphorylating a residue with Amber ff
- please help
- Please read: fatal error namd 2.7b1 for Win32 Memory allocation failed on processor > 0
- PLUMED 2.0 announcement
- pmf command
- Polarizability Question!
- Poor scaling in NAMD simulations
- Possible bug or inconvenience
- postdoc position available
- postdoctoral position available in simulations of ionic liquids at NASA Ames
- Potential energy as collective variable
- Potential energy in the boundaries
- Potential of mean force calculation using colvars in NADM 2.9 package
- pre residues and ligands interaction
- Pressure in equilibration stage of MD
- Pressure problem to equilibrate NPT
- pressure profile calculation problem
- pressure profile calculations
- pressure profile freezing
- Preventing rotation of a protein
- Printing energy of selected atoms in NAMD
- Problem during TMD
- problem in accelerated MD with NAMD-GPU
- Problem in creating dummy atom
- problem in determining atom types and charges for ligand atoms to type in the topology file
- problem in finding atom types for ligand
- Problem in running "Constant Velocity Pulling" example
- Problem in SMD "Constant Velocity Pulling" on Ubiquitin example
- problem in solvating a graphene layer created using VMD-nanotube builder
- Problem of 'missing stage' in colvars.state file
- Problem of ATP mutated to dATP in solution using FEP method
- problem of using SMD and TclForces keywords simultaneously
- Problem regarding the big DCD file
- Problem regarding the Pre-Minimizer Bad Contacts Removal
- Problem regarding the psfgen
- Problem running NAMD
- Problem running NAMD 2.8 with ibverbs
- problem to analyze the output of FEP file using vmd plugin
- problem with Dihedral
- problem with gpu namd 2.9b3
- problem with inorganic builder genCompressedPsf
- problem with installing NAMD in Linux Red Hat
- Problem with Methane-Methane PMF
- problem with NAMD surface area calculation (LCPO) -- fixed
- Problem with NVE simulation
- Problem with parameter file in Pair Interaction Calculation
- problem with paramters?
- problem with pdb pdf!
- problem with pdb psf files!
- Problem with psfgen for Carbohydrates
- problem with ptch ...
- Problem with replica exchange
- problem with restraining a dihedral angle
- problem with runiing namd through infiniband
- Problem with running FEP calculations
- Problem with the cross term of C NH1 CT1 C NH1 CT1 C NH1
- problem with using patch LINK ...
- Problems in setting up low pH systems
- problems with auto-psf gen and autoionize for ligand with atomtypes of more than 4 characters
- problems with simulation of LJ fluid
- Protein Dielectric Constant in GBIS
- protein folding by simulated annealing method
- protein folding by simulated anneling
- Protein ligand simulation Tutorial
- protein schematic representaton
- Protein unfolding and Coarse grained
- Protein-ligand affinity
- Protein-ligand simulation
- protein-water interactions
- Protonated nucleotides
- PSF file for a metalloprotein
- PSF files and long atom name
- psf generation error
- Psfgen - bonding terms involving disulfide bridges
- psfgen and CHARMM19 explicit exclusions
- Psfgen CTER issues
- psfgen tyrosine anion-Fe bond
- psfgen warnings
- pulling constant verocity
- pulling force didn't drop to zero in SMD
- pulling force doesn't drop to zero in SMD
- pump / force application
- puzzle of SMD in NAMD-2.9 and pull code in Gromacs
- QM-MM
- queries about "Tclforces" utility in NAMD
- Query about compressing PSF files
- query on constraintScaling in NAMD
- Query regarding NAMD
- Question about "Free Energy of Conformational Change Calculations"
- question about "useflexiblecell' command in NAMD operation
- Question about converting velocities DCD to ascii plain text
- question about dcd file
- Question about GPUs hardware.
- Question about how much used from CPU?
- Question about loading velocity files on VMD
- Question about NAMD
- question about NAMD on Kraken.
- question about NPT
- question about NVE ensamble
- Question about optmem input files
- question about relative binding free energy calculation method using FEP
- question about setting up FEP calculations
- Question about targetsNumSteps in ColVar
- question and NAMD operation
- question of MMPBSA calculation combined NAMD and APBS software
- Question of using deuterated water in NAMD
- question on explicit solvent reproducibility
- Question regarding FEP parameters
- question regarding interaction parameters
- question regarding simulated annealing
- questions about accelerated MD
- questions regarding ABF sampling in a DMPC bilayer
- Questions regarding pressure difference
- questions regarding the source code in NAMD
- R: restart file
- Random seed and equilibrated structure
- RATTLE algorithm
- RBCG-configuration file
- rcmd: socket: All ports in use w/ NAMD_2.9_Linux-x86_64-ibverbs
- RE : AW: vmd-l: Occupancy maps
- Reaction field treatment
- Reason: FATAL ERROR: DIDN'T FIND vdW PARAMETER FOR ATOM TYPE OT
- reassigning temperatures
- reassignTemp question
- ReaxFF and REBO
- Reduce percent use of cpu
- Reflecting boundary z axis in NAMD
- Reg Lack of Lack of VDW parameters
- Reg loadtotalforces.
- Reg Membrane Builder
- reg Parameters
- Reg Reading of files durin simulation
- Reg VDw Parameters
- Regarding Delta Delta G in FEP calculation
- regarding editing protonated glutamate in the pdb file via psfgen
- regarding editing protonated glutamate in the pdb file via psfgen . .
- Regarding installing Namd 2.9 on windows xp 32 bit system
- Regarding Installing NAMD in Ubuntu
- regarding ion concentration in implicit solvent
- Regarding Membrane Builder
- Regarding Production Run in NAMD
- Regarding the Protein-Ligand Free Energy Tutorial
- Regarding thermostats
- Release of ConcatXY
- Release of the R.E.D.-III.5 tools
- release the memory taking by the aotmselects/vars
- REMD and NAMD options
- REMD history file and question
- remd restart
- remd run command question
- REMD-GPU
- Remove tjwang@iastate.edu from the list pls
- Repelling extracellular regions of the protein from membrane in NAMD MD simulation
- Replica exchange - Temperatures and number of replicas
- replica exchange and colvars
- Replica exchange and colvars - Missing Stage from restart
- Replica exchange and multiple time-stepping
- replica exchange and replica.namd
- Replica Exchange Discrete Molecular Dynamics for structure based models
- Replica exchange on single physical node
- replica exchange parallel tempering BlueGene/Q
- Replica exchange, colvars & harmonic restraints
- Replica-exchange MD on a single node / SMP workstation
- Replica-exchange metadynamics scripts
- Resample trajectory files
- residue_rmsd.tcl via
- REST or RESTMD in NAMD?
- restart a simulation
- restart file
- Restart files are empy
- restart files not written.
- Restart simulation of an equilibrated bilayer with sugar molecules inserted
- restarting ABF
- Restarting Multiple Walker/Well Tempered Metadynamics
- Restarting simulation
- Restarting T-REMD with colvars
- restarting umbrella sampling simulation.
- restrain ligand in z-interval
- restrain ligand to z-interval
- restrain noe's in random.inp
- restraining
- Retaining conformation
- Reverse coarse-graining Error: CG Builder
- rigidBonds water and langevinHydrogen off (no problem!)
- rigidBonds water and langevinHydrogen off are INCOMPATIBLE when using a solute with hdyrogens
- rigidBonds water option
- RMSD calculation
- rmsd calculation in namd
- RMSD collective variable - Different atons to align and to calculate RMSD
- RMSD difference on alignment of two states of protein in VMD and NAMD TMD
- RMSD metadynamics
- Run NAMD binaries
- run NAMD command in GPU
- Runaway cuda-enabled namd2 processes
- Running fulldirect in parallel
- Running NAMD in multiprocessor single machine
- running namd in parallel
- running NAMD on Amazon EC2?
- Running NAMD on Forge (CUDA)
- Running namd on linux in cpu+gpu mode
- Running NAMD on SGE cluster - multiple modes and cores
- Running Parallel Jobs Simultaneously with MPIRUN
- running simulations on different machines with different versions of NAMD
- Rckruf: scnb value to prevent VDWs scaling
- Same NAMD files give error in Linux but not in Windows ....
- Scaling on 64 core nodes?
- Scaling problem: 4 nodes OK, 5 fails to start
- Scaling problem: 4 nodes OK, 5 nodes fail
- scnb value to prevent VDWs scaling
- secondary structure analysis
- secondary structure restraints in coarse grain
- segmentation errors
- Segmentation fault - colvar
- segmentation fault with NAMDenergy
- Selecting GPU for namd2
- selecting multiple fixed atom in SMD
- Separate water coordinates from graphite
- Set up NPT simulation in cubic PBC-box
- setting the polarizabilities for the Drude force field
- Sevoflurane parameters (psf file)
- SHAKE Tolerance and Performance
- Sherical BC energy conservation
- Shift (or offset) of the lipid bilayer along Z axis during equilibration
- shift the molecules
- Should I use a precompiled binary?
- Should the windows for ABF calculations be overlapped or not?
- Simulated Annealing for a polymer
- Simulated Annealing/ Cooling
- Simulation at different time-steps
- Simulation at high pressure
- Simulation Box Deformation
- Simulation continuously crashes after minimization
- simulation crashes frequently with "atoms moving too fast"
- Simulation in Collective sub-space
- Simulation in NPT ensemble
- Simulation of a protein and calcium ions
- Simulation of a protein and ions
- simulation of non-rectangular surface
- Simulation of Protein with Ions
- Simulation of the membrane protein
- Simulation results from NVT has a cavity
- Simulation Using Both NAMD and VMD
- Simulations with alpha methylated amino acids
- Simultaneous calculation on CPU-only nodes and CPU/GPU node (with or without rCUDA)
- simultaneous simulation for protein in water and SMD
- Single point energy calc with gaussian/namd... log file interpretation
- Slow vacuum/GBIS simulations (time to completion keeps increasing)
- SMD and torque application
- smd force is too high
- smd simulation
- smd tcl script - problem atoms id
- SMD under NPT ensemble
- SMD-DNA : ABNORMAL EOF FOUND - buffer=*END*
- smd-tclForce intrerface
- SMD: Compressing a Molecule
- sn-1 tail order parameter
- solvated system for minimization
- solved inputPrefix for ABF
- SOLVED: Fatal Error by charmc.../usr/bin/ld: cannot find -lsrfftw. Please help!
- SOLVED: Issues with the "Keep Water Out" tcl script
- Solvent Box
- Special constraint on MD simulation
- Specific colvar component needed.
- spectrum simulation
- spinAngle
- Sr2+
- src/ComputeNonbondedCUDA.C:1022: error: thread-local storage not supported for this target
- startup phase 8: not complete!
- Steered MD along detected routes
- Steered Molecular Dynamics tutorial
- steered molecular dynamics with multiple molecules
- stereo-chemical inversion during MD
- strange result using implicit solvent
- Stray PME grid charges on increasing number of replicas and T-range with T-REMD
- structure changing
- Subject: Simulated Annealing/ Cooling
- subscribe
- Sudden energy drop after minimization
- Sudden jumps during FEP
- Sufficiently large values for 'firsttimestep' can lead to immediate simulation abort.
- Suggestions on parameterizing a ligand to simulate in NAMD
- Suggestions while building a GPU-machine (CUDA) for NAMD use!
- suppressing LBD output
- surfaceTensionTarget - Surface Tension per interface or per bilayer
- Sutton-Chen potential
- Switching function while using AMBER force field
- symmetry restraints
- system splitted
- Tabulated potential
- Tabulated potentials - regd
- Tail order parameter
- target pressure value
- Targeted and Steered MD: Why must the initial and targeted PDBs have identical # of atoms?
- Targeted Molecular Dynamics
- TAU profiler with NAMD2.9 smp mode
- tcf forces and ccordinate wrapping
- tcl script for rmsd
- tcl-related segfault in NAMD
- tclBC incorrect output
- TclForces and efficient PBC corrections
- TclForces clearconfig cancels addforce calls?
- Techinal problems with ABF simulations
- Temperature reassignment
- testing digest demime - please ignore
- testing digest demime - please ignore #2
- Tetraphenylphosphonium
- the fictitious force or the viscosity of water
- The simplest pair list generation scheme
- The size of a periodic cell in NAMD operation
- The structure files for the second turn of simulation
- thernodynamics integration in NAMD
- Three GPU cards on shared-mem motherboard
- Timeline
- TIP4P force field
- TIP5P simulation
- TMD output format
- Topology and parameters for nitrate and nitrite ion
- topology file for ligand
- topology/parameter files for biotin
- total charge of the system - rounding error ?
- TOTLAL2, POTENTIAL abd aMD
- transmembrane protein simulation - hydrophobic thickness and NAMD membrane plugin
- Treating Multi Chain Proteins
- Trouble loading frames from large DCD files
- Trouble using rotateReference, centerRefrence and refPositionsGroup in the colvar module
- Trying to run a setup with amber force field in NAMD
- Two dimensional ABF
- Two GPU-based workstation
- typo/my flawed thinking on "alchVdwLambdaEnd"?
- Tyrosine ligand at Fe(II)
- umbrella sampling
- Umbrella Sampling after multiple replicas metadynamics
- Umbrella Sampling plus restraints
- Umbrella Sampling Replica Exchange Simulations
- Umbrella sampling using dihedral angle
- Umbrella sampling with hbond
- Umbrella sampling-reliability of results
- Unable to reproduce same results in minimization with GBIS
- Uncovering the Elusive HIV Capsid with Kepler GPUs Running NAMD & VMD
- understanding the energy term in NAMD log file
- understanding the lone pair section of psf files
- understanding which is which with GPU cards
- Uneven sampling in using ABF
- Uneven sampling when using ABF
- Unexplained segmentation faults in NAMD 2.9 using CUDA and GBIS
- units of pmf files
- unreasonably high temp/pressure
- unreasonably high temp/pressure. .
- unrecognizable code in the output file of ParseFEP analysis in VMD 1.9.1 under the Linux system
- unsubscribe
- unsubscribe from mailing list
- unsubscribe namd-l
- unsubscribe please!
- unsubscriber e-mail office pool anybody?
- unsuscribe
- use of colvars to restrain the absolute positions of all atoms in a large system
- User-defined forces in NAMD
- using CHARMM22STAR forcefield in NAMD
- Using CNS parameter file to create NAMD topology and parameter files
- using colvar for umbrella sampling between two carbon nanotubes in aqueous dispersion
- Using CosntantArea in membrane simulation
- Using Measure SASA in NAMD Simulations
- Using negatively charged phopspholipids and no neutralization, membrane expands in the xy direction .......
- Using negatively charged phospholipids and no neutralization, membrane expands in the xy direction .......
- Using TCLforces to rescale force(s) on particular atom(s) --- loadtotalforces, addforce and previous/current timestep issue
- Using volmap to calculate the water density around certain residues
- utilizing mic coprocs on Stampede
- vacuum minimisation-reg
- Vacuum simulations
- VDW component: NAMD vs. CHARMM
- VDW energy is negative but total energy is positive
- vdwForceSwitching and PME
- velocity distribution
- Very long simulation
- vibrational modes calculation
- vmd-l: About PLUMED with NAMD VMD
- vmd-l: connect a spring between all the atoms present in pdb structure
- vmd-l: Error with show_replicas.vmd
- vmd-l: FFTK Atom types
- vmd-l: FFTK VMD plugin issue (arising from VECSCALE TCL issues of either NAMD or VMD ?)
- vmd-l: fftk-charges
- vmd-l: Gromacs analysis tools for Namd output
- vmd-l: namd/vmd support to GTX-6## series
- vmd-l: Stand-alone VMD ?
- vmd-l: Suggestions on parameterizing a ligand to simulate in NAMD
- vmd-l: vmd installation problem
- VMD_waterbox
- W and S
- Warning & error
- Warning: Not all atoms have unique coordinates
- Water bubbles in NVT equilibration dynamics
- Water density in the solvate plugin
- water layer in membrane protein modeling
- water molecules
- water parameters
- weird energy values of LJ fluids
- Weird energy values of LJ fluids simulation
- WG: questions regarding the source code in NAMD
- WHAM analysis for Umbrella sampling
- WHAM in the NPT ensemble
- What does "outputSystemForce" output?
- what does .inp do from CHARMM GUI?
- What is a good (small) test system for NAMD
- what is fullSamples?
- What is the means of system-min.conf in the Residue-Based Coarse tutorial?
- what restraint can I use to prevent membrane diffusion on the Z-axis?
- what to do with this error
- What's the difference between upperboundary and upperwall?
- where does the second boost in accelMDdual mode refer to
- where is psf develop in ffTK
- Why does my volume suddenly expand as I increase temper ature.. .
- Why does my volume suddenly expand as I increase temperature.
- will Jaguar enough for NAMD partial charge?
- Will there be a NAMD2.9 for IBM AIX UNIX?
- win64 namd cuda: compile?
- Workshop - Computational Molecular Physics of Non-Bonded Bio-Molecular Interactions
- Workshop for Computational Chemistry & Physics
- Workshop In Aspen Colorado - Molecular Physics of Non-Bonded Biomolecular Interactions
- Workshop on GPU Programming for Molecular Modeling, August 2-4, 2013, in Urbana, Illinois
- wrap dcd files
- Wrapping
- writedcd problem
- Writing an output file into pdb format in a simulation.
- xplor psf used for namd
- XY constraints with center of mass movements
- zero mass particles in NAMD
- zeroMomentum for water droplet
- zinc finger with ASP
- 回复: Shift (or offset) of the lipid bilayer along Z axis during equilibration
- :
Last message date: Tue Dec 31 2013 - 11:28:27 CST
Archived on: Tue Dec 31 2013 - 23:24:07 CST
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