NAMD-L: By Subject
By Subject
4323 messages sorted by:
[ author ]
[ date ]
[ thread ]
[ attachment ]
About this archive
Starting: Fri Jan 02 2009 - 02:55:43 CST
Ending: Fri Dec 31 2010 - 20:32:36 CST
- "-Wno-long-double" linking error
- "didn't find VdW parameter for atom type NH3" error
- "gradient tolerance" for minimization
- "GroupPressure no" resulting in negative pressure outputs
- "Hands-On" Workshop on Computational Biophysics, July 6-10 and August 10-14, 2009
- "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
- "within" command in NAMD?
- 'dSmooth' no longer in the ABF procedure?
- (Infiniband-related?) NAMD 2.7b2 (ibverbs x86_64) runtime error during a MD run
- (is there) a dependence of dynamics on WRAPPING
- (no subject)
- (Á¦¸ñ ¾øÀ½)
- (âÅÚ ÔÅÍÙ)
- +1 offset to VMD index file?
- .inter.bin files?
- 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
- 2.7b metadynamics ::alpha module :: folding of a single helix in water
- 2.7b metadynamics ::hBond component :: folding of a single helix in water
- 2.7b1 + CUDA + STMV
- 32 bit + 64 bit mixed architecture problem
- 4 sequential jobs work on laptops, but only first one works on supercomputer
- 99999999.9999 as vander waals energy
- [***** SPAM *****] About APBS calculation
- [off topic] The mailing list's mailer ...
- [ppl] error compiling charm-6.2.2 for bluegenep-xlc
- A beginner's question for using NAMD to do cell membrane simulation and molecular transportation
- a cv-smd puzzle
- a gap in flowing water
- A problem of the forces-tutorial
- a question about modifying the NAMD input file
- a question about NAMD TI
- A script for performing calculations divided by quanta
- a timing question; 206,000atoms > 512cores not good
- ABF 'Xi' log output producing strange results
- ABF (NAMD 2.7x) speed ?
- ABF + LES
- ABF - sequence of MD runs
- ABF calculation - normalization of the PMF
- ABF calculation with TclForces script in the configuration file
- ABF calculations: Jacobian term describing geometry entropy
- ABF Colvars Configuration File
- abf convergence problems
- ABF Displacement
- ABF error calculation
- 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 (free energy partition)
- ABF questions
- ABF questions (Concatenate output files/force constant)
- ABF Simulation Crash from TCL script
- ABF simulations
- ABF tutorial
- abf with colvars example
- ABF-Zcoord:
- ABF: moving system in Z direction
- ABF:restraint in free energy calculation in Zcoord-method
- abf_integrate
- Abnormal EOF found -buffer=*END*
- abnormal water surface after nvt and npt for POPC membrane
- About "equilibrate.conf' of FEP tutorial
- About "Parameterizing a Novel Residue" tutorial problem
- About "Visualization and Analysis of CPMD data with VMD" tutorial
- About APBS calculation
- about calculation of PMF from SMD trajectories
- about calculation of PMF from SMD trajectories (with pasted smd_config_file)
- about compile namd2.7
- About CUDA version of NAMD 2.7 B1
- about DCD file format document
- About DPD
- about Hydrogen Bond correlation function
- about limitdist
- About matdcd
- about NAMD nonbonded routines
- About NAN error
- About plumed installation problem in NAMD_2.6_AIX-POWER-MPI
- about protein phosphorylation
- about psfgen
- about recentering of namd trajectory
- about restart
- About RMSD based PMF's
- About SMD
- About the err of "Constraint failure"
- About the err of "distanceZ"!
- about the memery lock in openMPI on infiniband
- About the namd tutorial err
- About the Nucleic Acid parameter and protein parameters
- About the solvate package
- About viscosity calculation
- Accelerated MD?
- Acceptance ratio of REMD simulation
- Accessing atoms and velocities during NVE run
- Acetyl group patch for lysine residue
- acridine orange
- Adding a new bond to CHARMM
- adding constraints
- Adding extra bond
- Adding special VdW parameters
- adding specific forces between atoms
- ADENOSINE-5-DIPHOSPHORIBOSE topology
- advice on van Hove
- alanine dipeptide: no dihdral energy terms?
- Alchemical calculations in CUDA version of NAMD?
- alchemical fep amber topology
- Alchemical FEP tutorial files
- alchemify with CMAP?
- alchemy FEP query
- AlF4
- Aligning the distance between two centroids with an axis
- Alignment of velocity dcd file
- Allowed CMAP dimensions
- Allowed CMAP dimensions in NAMD
- alpha character error in the psf file
- altering residues in .pdb files
- Amber ff99sb force-field in namd
- AMBER force field in NAMD
- Amber topology in CUDA NAMD - can it be done?
- 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 outlier appear on the curve of RMSD
- analysis of dcd
- Analysis of Results of only Lipid Bilayer Simulations
- Andres Morales sent you a little gift
- angle in colvars
- Angle in parameter file
- Announcement: TCBG workshop at Pittsburgh Supercomputing Center May 10-14, 2010
- anomalous behaviour of ASPP and GLUP during MD run
- Another strange error: MStream checksums do not agree
- any experiences with executing parallel NAMD in a NAMD simulation
- 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?
- Asking for some sample PDB and PSF files of carbon nanotube
- Aslos
- Assigning partial charges in topology file
- asymmetric water found!
- Asymmetric water molecule found
- atom charges for protonated carboxyl termini
- Atom constraint in certain direction
- Atom movement within a range of Z value
- atom type
- Atom type for protonated pyridine N
- atomic structure of some surfaces
- ATP and Stream files
- Automatic namd 2.7b1 installation
- Autopsf error with a modified top file
- AW: update: segmentation faults with AMBER topology and RAMD tcl scripts
- backbone restraints
- Background load problem
- Bad atom ID in extra bond file
- Bad global exclusion count
- Bad Global Exclusion Count Errors in (Relatively) Simple System
- Balancer and singularities ...
- base stacking analysis of the trajectory of a nucleic acids simulation
- benchmarking on Cray XT4
- Benzene PSF
- berendsen thermostat
- Berendsen, explicit water
- Berendsen- two baths
- Best tool to use to generate a custom (patched) polypeptide PDB?
- beta column
- bicarbonate parameters
- Bin Coordinate file to pdb
- binary trajectories
- Bioinformatics Symposium at C-DAC, Pune
- biotin parameters and topology
- blank between nanotube and the bulk water
- bonded FAD topology file
- bonding in periodic boundary conditions
- bracket in the log file
- Bringing UMA-type mainboards to TESLA
- Bug advisory: ABF integration tool
- Bug advisory: RMSD and ABF
- bug or custom?
- bugfixes in the colvars module (ABF, metadynamics etc.)
- build a layer
- build a wall
- build nanoparticle
- building a MARTINI bilayer
- BUILDING BPTI
- Building NAMD for Opteron Cluster with ICC
- Building PSF file for protein with ions
- calculate side-chain dihedral/torsion angles
- Calculating displacement in a system with periodic boundary
- calculating energy for large log files
- calculating forces from dcd trajectory
- Calculating interaction energy in NAMD
- calculation of periodic box
- calculation van der Waals force field parameters
- Can AMBER topology be used in NAMD-CUDA?
- can I change coordinate before restart?
- Can I get the pressure value in a cube?
- Can I use another solvent rather than TI3P model in namd for MD simulations ?
- can we control the number and distribution of solvate molecular
- CAN'T FIND BOND PARAMETERS FOR BOND C - CPB IN PARAMETER FILES
- Can't find C-PDB bond parameters
- CAN'T FIND DIHEDRAL PARAMETERS FOR CN8B CN7 ON5 HN5
- can't load forces in tclforces
- Carma v.1.0 released.
- Cartesian vs dihedral angle space PCA
- CatDCD installation
- Cationic Dummy Atom models
- cell basis vector restart
- Cell Data in DCD files - CHARMM compatibility
- cell on namd 2.7b1
- center of mass for SMD
- Center of Mass Harmonic Potentials
- center of mass of dummyAtom in colvar
- CG bead definition
- CG equilibration recurring crashes
- cg protein folding
- CGMD ? Hydrophobic scale
- cgmd stability
- change force field in NAMD
- change solvent
- Changing functions without recompiling
- changing protonation states for a pdb with more than a single polypeptide
- Changing the atomtype of a particle on the fly
- Changing the Potential Energy Function
- charge calculation
- charges in psf and in namd (or vmd)
- CHARM parameter file needed for simple organic molecules like Methanol, Formamide, Chloroform, TCE, Toluene
- charm++ build problem
- charm++ how to handle SMP/Multicore
- charm27 forcefield_topology
- Charmm carbohydrate force field
- CHARMM FF parameters for O2 Gas
- CHARMM Lorentz-berthelot mixing rules
- Charmm parameters for
- CHARMM to NAMD
- Charmrun/INTEL MAC/2.7
- Charmrun: error on request socket--
- Check out my photos on Facebook
- cholestrerol
- claen water
- Clarification regarding some finer details in ABF simulations
- CMAP dimension limited to 24 dimensions
- CMAP dimensions in NAMD
- CMAP in NAMD output
- CMAP w/ D-amino acid
- CmiAbort+0x5f
- COARSE GRAINED WATER MODEL
- coarse graining
- coarse-grained model building
- collective variable space PMF, including biasing potential terms?
- collective variables
- colvar atom syntax
- colvar error
- colvar for PMF calculation
- colvar module question
- Colvar on 2.7b2 win vs Linux MPI instalation
- colvar: atom group defn. fails
- colvar: coordnum output
- Colvars and COM restraints for protein+membrane; plus a minor bug
- Colvars Configuration File
- colvars don't run with minimization ...
- colvars error running ABF
- colvars fixes
- Colvars in NAMD 2.7b4
- colvars-history file
- colvars: Error: in parsing "centers"
- colvars: Error: undefined output or restart file.
- colvars: free energy change with rmsd
- Colvars: Using "Alpha" Component
- colvarsInput filename problem
- combining abf reaction path
- combining segments
- Comparision of GPU and multi-CPUs version of NAMD
- compilation error "could not set locale" with intel 11.0
- compile NAMD 2.7b1 on Intel Xeon(R) infiniband cluster
- compile NAMD with TCP and SMP
- compile namd2.7b1 on infiniband
- Compile Problem
- compiling error of NAMD2.7b1
- compiling NAMD failed on windows with Cygwin
- compiling namd gpu
- Compiling NAMD on Ranger
- Compiling NAMD under SGE and OpenMPI
- compiling NAMD w. infiniband
- conf file for coarse grained simulation
- configuration file
- Confira meu perfil no Facebook
- Conjugate gradient reference
- Consecutive Simulations
- Constant pressure
- Constant pressure simulation: can I get the changed volume?
- constraint energy contributions
- Constraint failure in RATTLE algorithm - shouldn't a rerun fail at the same step?
- Constraint failure in RATTLE algorithm for atom 268
- Constraint Failure in SMD simulation
- Constraint failures and TI electrostatic calcs
- constraints
- Constraints in NAMD
- Constraints on the plane and on the atom positions (in the same simulation)
- constraintScaling to gradually release harmonic restraints during minimization
- Continuing simulation after constraint failure error?
- Control DCD file
- convergence of ABF
- coordinate not the same between the input and frame 0
- Coordinate Output in both binary and ASCII. Or converting binary to ASCII in the command line
- coordinates and cells
- Copper parameters for CHARMM
- Correlation matrix of the Ca atoms
- Could namd realizes the QM-MM method?
- Could namd support the ATI-GPU
- Could namd use the method ONIOM of Gaussian?
- couldn´t find rsh program
- counting h-bond in system with vmd
- CPU GPU comparison
- CPU USAGE
- CPU usage when exec function is used
- crash
- crash with more than 96 processors (v2.7b1)
- Crashing ibverbs binary of NAMD_2.7b2
- Creating a NAMD Shared Library -> Undefined Symbols in Charm libs
- creating an output file from a dcd file
- Creating bonds during a run
- Cube vs. Truncated Octahedron Performance
- cuda 1.0 binaries on cuda 1.1
- Cuda benchmarks namd2.7b1 - effects of configuration parameters and hardware.
- CUDA error in NAMD 2.7: Increase MAX_EXCLUSIONS
- CUDA error memcpy to exclusions: invalid argument
- CUDA Linux-x86 doesn't compile
- CUDA on Win32 NAMD
- CUDA version status
- CUDA-accelarated NAMD does not use the video card?
- CUDA-accelerated NAMD does not support NBFIX parameters
- CUDA-accelerated NAMD does not support NBFIX parameters [RESOLVED]
- CUDA-NAMD hangs -- check the Northbridge temp!
- cutoffs in direct and indirect space used in PME?
- cvs logs
- Cylindrical harmonic BC and constraintScaling
- dcd
- dcd]
- DCOLVARS_DEBUG
- Debug NAMD with CharmDebug
- defenestrate
- defined path for NAMD2
- Defining Temperature for Langevin for Namd restart.
- Definition of two colvars for ABF
- Definitions of certain routine names in source
- degrees of freedom
- Denied permission on dcd file preventing simulation
- Deprotonated Lys
- Developing a neutral arginine patch in a topology file
- Dielectric Constant
- dielectric constant assignment
- dielectric parameter?
- Difference between Linux-x86_64-TCP and Linux-x86_64
- Difference between the two Dowsers
- Different Dielectric constant value for different segment
- Different ensembles in the same system
- Different types of constraints at the same time
- different values of "1-4scaling" in a system
- diffusion / fex peptide problem
- Dihedral angle energy in silica block
- Dihedral angle potential energy function
- Dihedral parameters for side-chains?
- Dihedral Restraints during MD simulation
- dihedral terms for a parameter file
- display all frames simultaneously
- dissociated quartz SiO2 groups in surface
- Distance Analysis for Constant Force Pulling for kinesin neck linker
- distance colvar
- Distance constraint
- Distance Restraint
- Distribute Points Evenly on Surface of a Sphere
- dmpc bilayer
- Do top_all27_prot_na.inp and cornell.prm share the same naming rules of atom types?
- documentation on parallel implementation
- Does "rigidbond off" work instead of "rigidbonds none"
- Does amber force field in NAMD 2.7b2 work stable?
- Does Berendsen increase viscosity of water?
- Does CHARMM stabilize alpha helices?
- Does NAMD have any capability to assign coordiantes to novel sequences?
- double-wide sampling with soft-core
- Doubts and problem in ABF simulations
- Dowser
- Dowser with RESIDUE LYR
- Dreiding parameters
- Drift of the center of mass of lipid bilayer
- Drude polarizability parameters
- dual all-atom/coarse grain simulation
- dummy atom mass changed
- duplicate residue key ALA will be ignored
- elastic network
- electric field along z-direction
- electric field unit conversion
- Electrostatic Potential Problems, WRT Minimizations
- electrostatic vs van der waals
- END: No log file
- Energy drif in NVE ensemble
- Energy minimization failure
- Enhance electrostatic interactions?
- Enthalpy calculation
- Enthalpy calculation from NPT simulation
- Equilibration "substraction" from obtained PMF from MD
- equilibration script from restart files
- erergy gradient tolerance in Configuration Files
- 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 : DIDN'T FIND vdW PARAMETER FOR ATOM TYPE C11
- error codes: 255
- error compiling charm-6.2.2 for bluegenep-xlc
- error during charm-6.1.3 building
- error during heating of the minimized system: (please reply!)
- Error generating file.psf for cholesterol, missing coordinates in file.pdb.
- Error in configuration file
- error in install NAMD_2.7b2_Linux-x86_64-CUDA
- Error in Minimization
- Error in running minimization
- error in scripting
- error in writing restart files
- error of the energy output when equilibration
- Error on renaming file: Permission denied
- error running namd
- Error running NAMD on CUDA
- Error running simulation on KRAKEN XT5
- error termination
- error while running config file
- Error with GUI NAMD Energy
- ERROR! Explicit exclusions or fluctuating charges not supported, atom ignored.
- Error: atom group "group1" is set, but has no definition
- ERROR: Atoms moving too fast with RBCG model
- ERROR: Constraint failure in RATTLE algorithm for atom
- ERROR: Constraint failure in RATTLE algorithm for atom 1880!
- ERROR: Constraint failure in RATTLE algorithm for atom 9080!
- Error: failed on end of segment with RBCG
- ERROR: Multiple definitions of 'LangevinPiston'
- ERROR: Stray PME grid charges detected
- 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
- eucb - beta testers wanted for trajectory analysis program
- evaluating energy in a trajectory of variable box size?
- Evaluating kinetic energy from a modified DCD file
- ewald self energy
- exclude 1-2
- exclude 1-2 or 1-4?
- Excluding interactions?
- Exclusions and CUDA
- Exiting prematurely
- expansion of solvation box at high temperature
- Explicit Water System Condensing
- extending namd / shared library build (UNCLASSIFIED)
- Extract trajectory from replica exchange simulation
- extracting info from output files
- FAD topology and parameters of FAD
- FAD-parameters
- fail to run replica exchange on more than one node
- Fatal Error by charmc - Compiling NAMD_2.7b2_Source
- Fatal Error Help
- Fatal error in configuration file
- Fatal error when running ABF simulation
- FATAL ERROR: ABNORMAL EOF FOUND - buffer=*0 0 0*
- FATAL ERROR: ABNORMAL EOF FOUND-buffer
- FATAL ERROR: Asymmetric water molecule found??? This can't be right.
- FATAL ERROR: Bad global exclusion 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: Couldn't open DCD file ubq_wb_eq.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: Duplicate bond
- FATAL ERROR: ERROR(S) IN THE CONFIGURATION FILE
- FATAL ERROR: FixedAtoms may not be enabled in a script
- FATAL ERROR: Periodic cell has become too small for original patch grid!
- FATAL ERROR: Setting parameter constraints from script failed!
- FATAL ERROR: Sorry, combined TI and FEP is not implemented
- fatal error: tried to assign bond index before all parameter files were read
- FATAL ERROR: Tried to find atom type on node other than node 0
- FATAL ERROR: UNABLE TO FIND ANGLE PARAMETERS FOR HT HT OT
- FATAL ERROR: UNABLE TO FIND ANGLE PARAMETERS FOR NH3 HC NH3
- FATAL ERROR:BAD GLOBAL EXCLUSION COUNT:Please help
- FEP and GPU
- FEP anomaly?
- FEP calculation is doing nothing
- FEP for GLY and PRO Mutations
- FEP implementation in NAMD 2.6 vs. 2.7b1
- FEP on 2.7b1
- FEP on NAMD2.6 versus latest CVS NAMD build
- Fep performance
- FEP restart?
- FEP simulations?
- FEP substrate transformation with common moiety
- FEP to replace a PMF calculation?
- FEP tutorial graph question
- FEP VdW and electrostatic decoupling parameters
- FEP with fixed explicit environment?
- FEP yields the same results for forward and backward computation!
- FEP/binding free energy difference WT vs Mut
- Fermi NVidia
- FFTW and NAMD problems during compiling on BluegeneL
- file writing stopped
- finding appropriate topology file for polymers
- Finer details of an ABF/colvar simulation
- firsttimestep in NAMD
- Fixatoms minimization problem!!
- fixed atoms pdb
- fixing parts of an equilibrated protein's environment
- fixing the protein during minimization
- flashmob namd
- flexible-cell constant pressure not supported in CUDA
- flipdcd
- Flushing memory into output file
- followup question on error calculation in ABF
- for your suggestions on Pressure Control of transmembrane protein (GPCR)
- force constant in abf configuration file
- Force constant scaling
- Force Constant Units
- Force extension from SMD log file
- Force field for PDMS
- Force field for replica
- force field for replica exchange with NAMD
- Force Fields
- Force on multiple atoms in ABF
- force output of pairInteraction
- force-field for ATP
- force-field for cy3, cy5 dyes
- Forces on Atoms and Potential Energy
- Format of namd restartfile *.coor, *.vel) (2nd try ;) )
- Formating of logfile
- Free Energy Calculation of a protein
- Free energy calculation yields strange results
- free energy changes of one subunit
- Free energy of conformational change
- Free energy perturbation (FEP) hybrid pdb file
- Free-energy perturbation in NAMD: Evaluation of electrostatic and van der Waals terms
- FreeEnergy and minimization
- FreeEnergy: Not enough steps to complete pfm & mcti blocks
- fresh file not ready to read?
- frozen water Oxygens
- Fullerene topology
- Fwd: 99999999.9999 as vander waals energy
- Fwd: Coarse Graining Problem
- Fwd: conf file for coarse grained simulation
- Fwd: electric field unit conversion
- Fwd: error : atom moving too fast
- Fwd: Error in Minimization
- Fwd: error in scripting
- Fwd: force constant in abf configuration file
- Fwd: help to improve the script to predict mean square displacement
- Fwd: Installing NAMD on windows
- Fwd: Job submission to Lonestar on TACC
- Fwd: minimization problem
- Fwd: Minimization problem of a protein-DNA complex with namd
- Fwd: one atom off in the minimization result
- Fwd: Periodic cell has become too small
- Fwd: PROBLEM OF INSTALLATION OF NAMD
- Fwd: psf file creation
- Fwd: RBCG tutorial
- Fwd: reading prameter file
- Fwd: RESP and CHARMM
- Fwd: Running a simulation with coarse-grained protein in membrane
- 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: Tried to find atom type on node other than node 0
- Fwd: vmd-l: CG bead definition
- Fwd: vmd-l: Restraints on coarse grained model
- g(r) calculation for CNT
- g(r) GUI Plugin problem
- GeForce vs. Tesla
- Generate missing atoms of a coarse grained structure
- Generate psf files from Scott Feller's lipid coordinates
- Generating binvelocities, bincoordinates, and extendedSystem files (AMBER)
- Generating psf for NPC1
- generating xsc and vel files
- Generation of .psf file of DNA
- Generation of average trajectory
- geomtery optimization with namd
- get total force on a group of atoms within GlobalMasterSMD
- getting desired angle
- glibc detected : corrupted double-linked list: 0xa4657ad8
- glibc runtime errors on BlueGeneP occur only if running the cvs code (18.08) and not namd 2.6
- global and internal motion of protein
- GPGPU Programming summer school at University of Tennessee, Aug 10-14.
- GPU heavy models?
- gpu pressure control
- GPU Selection in NAMD CUDA
- gradient tolerance
- Gradient tolerance nan for A three-atom simulation
- gradual increase in the temperature after minimization
- Grid Forces
- Grid Forces documentation
- grid-based correction map
- GridForces methodology in NAMD 2.7b1
- Gromacs simulation not running in NAMD
- Group forces in tclForces
- GTP topology file
- H-bond and salt bridge between protein dimer
- Hardware for NAMD / VMD machine
- harmonic constraint when equilibrate the system
- Harmonic restraint parameters
- Harmonically constrained simulations
- headgroup area calculation
- heating a system
- heating and binvelocities
- Helix tilt
- Hello!
- help
- Help pls: Got error on FEP calculation: ERROR: The following variables are NOT VALID lambda2...
- help requested
- help running NAMD energy at multiple stable temperatures (newbie)
- help whit distance restraint
- Help with cys unprotonated
- help with running namd-cuda for the tutorials
- help with the equilibration script
- Help: NAMD on cluster; nodes reject multiple connections
- Hepl whit colvar subrutiene
- Hexafluoro-2-propanol (HFIP) force parameters
- hexane
- hi
- Hi,all, the parameters for Strain
- high atom velocity
- high pressure
- High RMSD in Coarse Grain Simulation of Protein
- High RMSD of Coarse grain Protein
- highthroughput NAMD
- Histamine topology file
- hole on the surface of the waterbox
- How are the SMD atoms connected to the center of mass
- how best to build a GPU-accelerated desktop machine for NAMD?
- How can I connect different structures between them using VMD and NAMD?
- How can I find topology and parameter files for heterocyclic, heteroaromatic, halogens and sugar compounds
- How can I fix lipid lateral area in membrane simulation?
- how can i get the energy of a molecule of a whole system?
- How do I connect the non-overlwindows of ABF's results?
- How I can insert de harmonic restraint?
- How is dG caluclated from dE during FEP?
- How the seed influences the molecular dynamics simulations?
- How to access velocity coordinates from within TclForces script
- How to acetylate at the N terminus and amidate at the C terminus
- how to add ions to a system
- how to add ions to a system/DASHOFSALT
- How to analysis RAMD data?
- How to apply an unsteady magnetic field?
- how to apply restraints for phi and psi for alpha helix regions
- How to calculate binding free energy of a protein-DNA complex by using NAMD?
- How to calculate free energy for conformational change
- how to cenvert NAMD binary coordinate file to text file
- how to config two different files for fixed atoms
- How to confirm water box is big enough?
- How to convert the GROMOS parameter unit into charmm22 style
- How to do a complex dynamics simulation
- how to do a MD of small part of a protein, using namd?
- how to do: FEP e2?, a protonating mutation?
- how to ensure molecules adopt their favor orientations in SMD simulation
- How to fix relative position of a group
- how to generate DNA psf files?
- 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 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 over with the error "Atoms moving too fast; simulation has become unstable and Exiting prematurely
- How to get PMF from SMD with colvars
- how to get psf files of DNA but not RNA with psfgen?
- how to get rid of TCL messages in namd.log from tclForcesScript
- How to get the acceptance ratio in REMD
- How to get the coordinate of a certain atom with tcl in the config file?
- how to get topology and parameter file for ligand
- how to improve the occupation of GPU with NAMD-2.7b3-CUDA
- how to install namd in windows xp
- how to install NAMD on suse10_ppc64 without xlc
- How to minimize our model by SD using namd
- How to obtain the system force on a fixed atom
- how to output the velocity for one selected atom in the system
- How to prevent cg water entering a membrane
- How to put a COM restraint on a membrane protein?
- How to read trajectory within CHARMM generated by NAMD
- How to restraint angle in NAMD
- how to run namd2.7b1 on multiple nodes
- how to save a DCD file without water in NAMD ?
- how to save a DCD file without water in NAMD: COMMAND LINE
- how to save output file in plain text?
- how to save pdb file after "moveby" command in VMD?
- How to set improper dihedral for trans-double bond.
- how to set initial velocity?
- How to set magnitude of cellBasisVector?
- how to set pH
- How to set the parameters for C60?
- How to set the parameters for two different baths in one molecule?
- how to set up force parameters of a novel residue?
- how to simulate a protein-ligand complex ?
- How to solve the out of cell box for long time in Periodic Boundary Conditions?
- How to specify processors for running VMD on a cluster?
- how to submit job on a HPC equipped with infiniband
- how to use constraints properly
- how to use ethanol as solvent in namd for MD simulations ?
- how to use ethanol as solvent in namd for MD simulations?
- How to use harmonic restraint parameter for 2 selection of atoms
- how to use hydrogen bond parameter during minimization and simulation
- How to use lset inside tclforces/calc_forces
- how to use volmap analysing a series of dcd.
- how to write a command to close vmd in shell script?
- How were the output files of the Replica Exchange Method sorted?
- how work: harmonic position "constraints" module + "WrapAll on"?
- HW - HW IN PARAMETER FILES
- hydration in membrane-protein simulations
- Hydrogen molecule model
- hydroxyls in phosphate group collapsing
- I can patch namd for amber ff on GPU
- I can't keep my pulling directions the same with the SMD vector
- I: Running Charm++ over MPI does not work
- iAPBS 1.0.0 released
- ibverbs crash
- IBVerbs NAMD build segfaults
- IMD VMD NAMD adding frames
- IMD, Hostname and Port
- Implementation of graphite walls
- Implementation of Martini CG FF in NAMD
- Implicit membrane models
- implicit solvent model in NAMD?
- implicit solvent with iapbs
- Importance of the Topology File, .rtf, and Other Files
- impose restraint on the internal coordinate of protein
- in NAMD tutorials: why "HSE" instead of "HSD"?
- inconsistence in NAMD and AMBER energy
- inconsistence in NAMD and AMBER energy: AMBER truncted octahedron
- Incorrect Atom Count
- Incorrect Atom Count in binary file
- increase the temperature step by step after minimization
- Info: Attempting to read FFTW data from FFTW_NAMD_2.7b1_Linux-Itanium-MPI-Altix.txt
- Inorganic compounds
- input file for memory optimised version
- Input/output error
- 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
- Intel 11 compilers
- Interaction energy difference
- Interaction potentials W-S
- interaction-energy
- Interactive MD driver/controller software no longer in beta
- Interactive protonation
- Interface analisis
- ion concentration in residue-based coarse-grained model
- Ionization with VMD
- Ionize script
- Ions conversion from atomic model to coarse grained model
- Is it a bug? TCL Script may Lead to Overflow
- Is it possible to run replica exchange simulation on BlueGeneL?
- Is the DCD file size consistent for consecutive runs?
- 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
- issues with AutoPSF for a cyclodextrin
- issues with AutoPSF for a cyclodextrin - addendum
- Jarzinsky's equation
- Jarzynski equality and the pull direction in SMD
- Job Offer
- Job restart
- job script for Kraken
- job submission script on KRAKEN @ NICS
- Job submission to Lonestar on TACC
- jobs get stuck using NAMDv2.7 and stop producing output in the log-file
- K25 NIH award
- Kanamycin topology
- Kemp elimination substrate charmm parameters
- Keyword to start FEP calculation in NAMD 2.7b1
- lamboot -v nodelist
- lammps input data file
- Langevin Damping = 0?
- Langevin damping coefficient
- Langevin process in NAMD tutorial
- langevinhydrogen on with rigidbonds water
- langevinTemp and system temperature
- Large protein translation during minimization
- last call for 2.7b3 bug reports!
- launch NAMD from tcl script
- launch NAMD from tcl script - bug?
- LD with explicit water molecules
- Least squares fitting of frames of trajectory
- Lennard-Jones potential in CHARMM
- LES dcd file split
- LES problem
- ligand flies away from binding pocket
- ligand parameters
- Lipid and protein interactions
- lipid bi-layer and SiO2
- lipidmonolayer
- lipids moving
- LJ correction in NAMD2.7b3
- loading large dcd files
- loading of large dcd files
- Loadleveler Script on Bluegene for NAMD
- Local elevation method in NAMD?
- location of the SMD source code
- log file from 3 different protein simulations
- looking for topology and parameters of methamphetamine
- Loop
- Low temperature Molecular Dynamics
- Lowe-Andersen thermostat
- Magnesium Ions Placement
- Make NAMD2.7b1 with cuda bug?
- mapping of force vectors during SMD
- maximum number of devices supported per namd process
- maximum residues using AMBER parm with NAMD
- MD papers
- MD simulations increasing electrostatic potential of a certain residue
- Measuring protein diffusion: results too small?
- Measuring the molarity
- Membrane Proteins Tutorial
- Membrane simulations
- membrane tutorial.
- memory allocation failed on processor 0
- Memory keep increasing.
- memory optimised version and exclusion check
- mercury ion parameters?
- Metadynamics in NAMD
- metadynamics simulations slow down and down
- Methylated Histidine topology file
- mgridforce
- Minimisation Protocol
- Minimization at higher temperature
- Minimization convergence
- Minimization convergence issue
- Minimization does not converge
- minimization gradient question
- Minimization issue.
- Minimization messes up C terminal
- minimization problem
- Minimization problem of a protein-DNA complex with namd
- Minimization problem on cluster
- MINIMIZER SLOWLY MOVING 810 ATOMS WITH BAD CONTACTS DOWNHILL
- MINIMIZER SLOWLY MOVING ATOMS WITH BAD CONTACTS DOWNHILL
- mininization do not go on
- Missing angle parameters CT3 CT3 CT3
- missing libraries for NAMD 2.7 on Linux cluster?
- Modeling familial amyloidotic polyneuropathy
- Modeling of Gramicidin A
- modification of CHARMM force field
- Modification of Colvar Module Components
- Modification of equlibrated simulation box
- Modification of equlibrated simulation box: OPTION 4
- modifying a nucleobase
- Modifying a peptide and introducing residues
- modifying velocities within global master
- Molecular dynamics of multiple organic molecules with NAMD
- molecular dynamics simulation
- molecule jumps from one site to the other?
- monitoring instantaneous kinetic energy of a subsystem
- monolayere
- MOnte carlo simulation
- morse potentials in NAMD revisited
- multi-cluster configuration
- Multi-step MD in a single .conf file
- multiple FEP experiments in one NAMD-FEP run?
- multiple trajectories
- multiplicity of dihedrals
- Multiplicity of Parameters for dihedral bond exceeded
- multistep minimization with different constraint
- mutation of DNA
- my problem was solved
- My protein went out of the water box in SMD. Would it have a bad effect on the result?
- Mysterious Formation of Solvent Spheres
- NADP
- NAMD 1.7b1 quits writing files/hangs
- Namd 2.6 on ubuntu 9.10
- NAMD 2.6, AMD64, MVAPICH2 compile error
- namd 2.7 iverbs error 93620 attaching to node
- NAMD 2.7 performance issues and Questions about Compiling
- NAMD 2.7 released
- NAMD 2.7b1
- NAMD 2.7b1 ABF + free energy windows
- NAMD 2.7b1 and clustermatic
- NAMD 2.7b1 distanceDir
- NAMD 2.7b1 on Abe
- NAMD 2.7b1 on Athlon64 Gigabit MPI - Compile Error "src/Settle.C:153: error: ‘_mm_cvtsd_f64’ was not declared in this scope"
- namd 2.7b1 on infiniband about the error : stack Traceback
- NAMD 2.7b1 on Lonestar
- NAMD 2.7b1 on NCSA Abe
- NAMD 2.7b1 on Ranger/MPI Problems?
- NAMD 2.7b1 on SGI Altix 330
- NAMD 2.7b1 on Teragrid
- NAMD 2.7b1 Performance loss with CUDA 2.3
- NAMD 2.7b1 release
- NAMD 2.7b1 running & performance issues
- NAMD 2.7b1 running problem
- NAMD 2.7b1 with APBS/iAPBS
- NAMD 2.7b1: metadynamics+tclForces => "... design error, GlobalMasterServer..."
- NAMD 2.7b2 new features
- namd 2.7b2 or later - amberff/prmtop causes segfault during startup phase
- NAMD 2.7b2 Released
- NAMD 2.7b2 versy slow on multiple nodes
- NAMD 2.7b2 with CUDA and infinband
- NAMD 2.7b3 released
- NAMD 2.7b4 released
- namd 2.7b: measure free energy difference "growing" a force constant
- NAMD and CFF forcefields
- NAMD and Gromacs
- Namd and MM-PBSA
- NAMD and multi-rail IB for improved latency
- NAMD and new sugar parameter set
- Namd benchmark problem
- NAMD bonded energy function
- NAMD cal with AMBER forces: Polarizable parameters in AMBER
- namd CG minimization error: unable to find angle parameters for nxg nxx nxg
- NAMD checkpoint mechanism.
- NAMD complain about gromacs ff parameter ATOMTYPES definition
- NAMD CONFIG FILE::
- NAMD CUDA
- NAMD Cuda NBFIX Terms
- NAMD CUDA on dual Nvidia 295 GPUs
- NAMD CUDA performance degradation
- NAMD CUDA release
- namd cuda with geforce 470 (fermi) gpu fatal error at runtime
- NAMD CVS
- namd cvs 26.06.09, tcl 8.5, loadcoords
- namd cvs compilation with a maximum number of cores to run on
- namd cvs memory leak?
- namd development mailing list?
- NAMD disk writes and quota overflow
- NAMD documentation regarding compiling
- NAMD Energy types
- NAMD error message
- NAMD FEP and GPU
- NAMD FFTW question?
- NAMD file limitation in Win32 - windows XP
- NAMD hanging on GPU
- namd hangs or exits with segmentation faults on opteron cluster with infiniband
- NAMD ibverbs not working on new cluster
- NAMD in TACC lonestar
- NAMD infiniband performance
- namd install
- NAMD installation
- NAMD is too slow?!
- namd job crashed
- NAMD job dies on 2-quad core server
- Namd lite
- Namd not detecting my CUDA enabled GPU
- NAMD on 64 bit windows 2007
- NAMD on a virtual grid
- NAMD on AMD Istanbul versus intel Nehalem with infiniband
- NAMD on current CPUs
- NAMD on GPU
- NAMD on linux
- NAMD on Ranger
- NAMD on Ranger at Teragrid
- NAMD on Ranger performance
- NAMD on Shared Memory (Altix UV 1000)
- NAMD OPLS Parameters
- NAMD Pair Interactions Finite Box Size Correction
- NAMD parralel processor windows
- NAMD performance with 10GbE interconnect
- NAMD regression test suite?
- NAMD running error
- 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 Tuning page on the wiki vs. NAMD/CUDA
- namd ubuntu-instalation
- Namd using Charmm restart files
- NAMD water sphere problem
- Namd with Amber ff for RNA minimization
- NAMD with CUDA
- NAMD with missing residues
- NAMD with Replica Exchange Simulations on Teragrid
- NAMD with two GPUs
- NAMD-CUDA benchmarks, dual GTX295, dual Xeon Nehalem system
- namd-cuda-intel vs. namd-intel
- NAMD-FEP tutorial-alchemify problem
- namd-openmosix
- NAMD-problem
- namd-SMD constant Force missing smdatom location
- Namd. Small molecules
- NAMD/metadynamics
- NAMD/VMD Research Programmer Position available
- namd2 still works but without any new messages in log file
- NAMD2.6 - 1D Periodic Boundary and PME - FATAL ERROR: PME requires periodic boundary conditions.
- NAMD2.7 scaling problems
- NAMD2.7/MEtadynamics simulation analysis disparity
- NAMD2.7b1 performance
- namd2.7b1 slower with openmpi 1.3.2 than namd2.6 with openmpi 1.2.6
- namd2.7b1 slower with openmpi 1.3.2 than namd2.6 withopenmpi 1.2.6
- namd2.7b1, tip4p, and dummies
- namd2.7b3 vs namd2.7b2
- namd27: tclforces activate TI calculation by default
- namd: Running namd on a node on cluster
- NAMD_ti.pl
- namdcvs
- NAMDenergy: does rewrite temp files at different timesteps
- NAMDEnergy: FATAL ERROR: Please add +idlepoll to command line for proper performance.
- NAMDv2.7 stops producing output in the log-file--any help?
- NANMA free energy surface vacuum map problems
- NBFIX and cuda
- need advices for running NAMD efficiently.
- Need Charmm FF for Gangliosides
- Need help preventing hydration of the lipid-protein interface in my system
- Need help to generate ubq-get-energy.conf
- new NAMD user ABF setup question
- New NVIDIA GPU C2050
- New open() for DCDs in v.2.6 ?
- Nightly build version: Parallel IO can not be used with langevin On
- No log file
- No. of processors in the namd command.
- nodelist file for concurrent execution of 2 nodes
- nonbonded potential
- nose-hoover
- NPAT - NPgT ensemble
- NPT simulation schemes
- Number of MC steps in ABF integrate gives entirely diferent surfaces
- NVE crash
- NVT with truncated octahedron or with sphere?
- O-PHOSPHOTYROSINE link to DNA base pair.
- Offset for frame ids in dcd trajectory
- on NAMD simulation of DNA translocation through nanopores
- On naming rules in force-field parameter files?
- one atom off in the minimization result
- OPENING EXTENDED SYSTEM TRAJECTORY FILE
- OPLS mixing rules
- Optimizing configuration option for fast calculations
- order parameter, lipid segments as vectors
- Output of forces
- outputname and restartname
- Pair interaction : Energy values are zero
- Pair interaction calculation - Direction of the force
- pair interaction calculations
- pair interaction energy for 2 water molecules
- pair interaction of water molecules
- Pair interaction runtime analysis skipping dcd frames
- pair interaction self in 2.7b3
- pairinteractions
- pairinteractionself in 2.7b3
- Par and Top files for BCL
- par_all36_cgenff.prm with NAMD2.7 - problem of file reading
- Parallel replicas?
- parallel scaling issues
- Parallel Simulations
- Parallel TMD (2.7b) dies : "MPICH internal error"
- PARAM22 and CMAP correction
- paramater about Amphotericin B
- Parameter File
- parameter file for carbon nanotube
- parameter file for CHARMM
- Parameter file problem
- parameter format for REMD simulations
- Parameters for esters
- parameters for Glutathione and BSO
- parameters for graphene nanoribbons annealed by hydrogen
- Parameters/topology entries for non-standard nucleotides
- Parametrizing a novel residue
- Paratool: where is "tip3.xbgf"?
- Particle Mesh Ewald question (from the tutorial)
- patch missing residues
- PCA Analysis of CGMD
- PCA Calculation
- pdb and rmsd
- pdb file
- pdbalias for PO4 residue
- Peptide in Membrane Environment: loosing water from one leaflet
- peptides on surface
- Performance peoblem about NAMD-CUDA benchmarks
- Periodic boundary condition in a membrane simulation
- periodic boundary conditions
- Periodic boundary conditions in membrane simulation
- periodic boundary conditions in namd energy calculation
- Periodic cell has become too small
- Periodic cell has become too small for original patch grid!
- Periodic Forcing Functions
- Phi MD
- phosphate parameters
- phosphoserine simulation using toppar files and NAMD
- Please disregard the spam "Lei sent you private photos on Tagged :)"
- plotting potential energy
- Plumed and NAMD
- PLUMED release 1.0.0 available
- PLUMED release 1.1.0 available
- PLUMED release 1.2.0 available
- PLUMED tutorial announcement
- PME and fixed atoms questions
- PME Kappa and Non-bonded Cutoff
- PMEGridSize
- PMEGridSpacing
- PMF via constrained dynamics in NAMD
- PMF: free energy calcs in "grow" phase?
- polymer topology file
- positive total energy
- possible bug with NAMD Energy plugin
- Possible way of performing a temperature gradient??
- Postdoc Position available
- Postdoc position in biomolecular simulation
- Postdoc position in computational biophysics and nanotechnology
- Postdoctoral Position in Scientific Computing
- potential functions in NAMD
- Precision of Coordinate data
- Pressure coupling and system heating
- Pressure is not constant in NPT ensemble
- Pressure parameter in minimization
- pressure profile
- Pressure profile calculation problem
- pressure profile calculations
- Pressure Questions
- PRESSURE, GPRESSURE, PRESSAVG, and GPRESSAVG
- problem about NAMD compile
- problem at applying patch
- problem at maintaining geometry coordinate
- problem caused by cluster?
- Problem compiling namd
- Problem Compiling NAMD (version 2.7b2)
- Problem facing during Solvation of Coarse Grain Model
- Problem generating psf file in psfgen
- problem in cgsolvate.tcl while adding CG water to the system
- Problem in energy minimization using Fixatoms or Constraints
- problem in fitting Maxwell-Boltzmann distribution
- problem in generating psf file
- Problem in minimization, Energy "-1.#IND" and bad dcd file.
- Problem namd2 and mpich2
- problem namd2-MPICH
- Problem of compiling Version Nightly Build (2010-02-16)
- Problem of running NAMD
- problem on pair interaction
- Problem on periodic boundary condition
- problem regarding rattle algorithm
- Problem running NAMD on ranger@TACC
- Problem to generate water segments and lipid reading in membrane
- Problem when using psfgen
- problem whit comand "COM"
- problem with cuda version
- Problem with extraBonds
- Problem with number of steps > 1000000
- problem with NVT using TIP4P
- Problem with Targeted molecular dynamics
- Problem with topology file
- problem with water
- problem wuth solvate plugin
- Problems about FEP simulation
- problems compiling charm and NAMD on intel cluster using MPI over ethernet
- Problems deciphering fepout
- Problems installing NAMD
- problems of "Stray PME grid charges"
- Problems with AutoPSF
- problems with CG protein-lipidbilayer-water system
- problems with NAMD plot and .DCD file
- Problems with OPLS in NAMD
- Problems with tcl scripts for REMD simulation
- problems with temperature control
- problems-protein minimization
- processor counts FFT and NAMD
- Proline hybrid topology file for FEP
- protein collapsing problem
- protein collapsing problem!
- Protein collpasing problem!
- protein fixed in simulation
- protein folding
- protein folding cg
- Protein in a Lipid Membrane
- protein shifts out of the water box
- protein shifts out of water box
- protein unfolding
- protein unfolding no increase in conf energy
- Proteine-membrane simulation.
- protocol to start MD
- Protonation
- psf creating for carbon nanotube
- PSF file
- psf file creation
- psf file error
- psf of insulin
- PSF/top/inp for joint charmm/amber benchmark
- PSFGEN
- psfgen creates too many bonds in a distorted Fe4S4 cluster
- psfgen error
- psfgen errors
- psfgen fails to set coords for all atoms
- psfgen gives wrong psf file
- psfgen problem, not generating angles/dihedrals
- Pulling atoms in different directions
- 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?=
- Query regarding ABF Tutorial on Methane Hydration
- question about cellBasisVector*?
- question about FEP soft-core
- question about NAMD
- question about repeating output text
- Question about Tcl/customising the colvar module
- Question for Developers: NAMD 2.7 performance issues and Questions about Compiling
- question on forces / theory
- question on hydrogen bond
- Question on mutator in VMD
- question regarding warning.
- questions about ABF simulations
- questions about Constant Pressure Control (variable volume)
- Questions about lattice information in NAMD2.7b2
- questions about smd
- Questions about thermodynamic integration in NAMD 2.7b2
- questions about user defined potential in NAMD
- Questions from new user
- questions regarding new single node box for NAMD: re components, CUDA, Fermi
- R.E.D.-III.3 tools release - q4md-forcefieldtools.org
- R: I: Running Charm++ over MPI does not work
- Radius of gyration
- RAMD in NAMD
- RAMD in NAMD; bugs and new version 4.0
- RAMD patch in NAMD CVS
- RAMD scripts and tcl version
- RAMD scripts version 4.1
- Random Expulsion MD (REMD)
- RBCG
- RBCG tutorial
- RBCG-dcd files
- RDF.tcl selections
- re a problem with "Charging a spherical ion"
- Re-posting - Methylated Histidine topology file
- Read dcd file and calculate (distance/constraint energy Vs snapshots) using NAMD
- Read DCD file in Java
- reading dcd file
- 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
- Reassign temp
- Reassign Temp during the Production Run
- reassignFreq script
- ReassignFreq script fail!!
- recalculating energy using dcd file
- recent papers on MD gotchas with PRNG seeds
- Recover high precision coordinates from binary .coor file
- Reference file for the constraining force in Umbrella Sampling
- reference of ewald method
- reg dynamics
- reg_membrane_peptide_interaction
- Regarding ABF Simulation
- Regarding amber parameters using NAMD
- regarding implicit solvent models
- Regarding ligand forcefield
- Regarding Lipid Order Parameter Calculation
- Regarding NAMD algorithm
- Regarding NAMD CPU usage
- regarding parameter and topology files for a new molecule
- Regarding Periodic Boundary
- regarding positioning of protein molecule
- regarding protein-protein interaction
- regarding psfgen algorithm
- regarding simulation
- Regarding temperature accelerated MD
- REGARDING Topology file
- regarding topology file generation
- Regd :parameter file
- Regd: Error
- regd: my parameter file
- Regenerating a .dcd file
- reinitvels vs restart.vel
- 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 on AIX5.3
- Removing some water from a .dcd file or .coor file
- removing water from big dcd files
- Replay to Parametrizing a novel residue]
- replica exchange trans cis isomerisme
- Reply: couldn´t find rsh program
- Request for information regarding ABF in NAMD.
- request help- namd error abortion stack error
- requirements for running the precompiled Linux-x86_64-ibverbs
- Rescale Temperature when velocity of COM is not zero
- RescaleFreq of temperature =1?
- residue based CG method
- residue based coarse-grained simulation
- Resources for trying out NVIDIA GPUs for free with NAMD
- restart ABF
- restart from different snap shots
- Restart MD from a certain point?
- restart REMD simulation
- Restart RMSD increase
- Restart simulation
- Restart, discontinuity of energy
- Restart, RMSD increase
- Restarting A NAMD job with velocity file
- restarting a simulation ?
- Restarting ABF
- restarting simulation
- restating simuation and periodic cell conditions
- restraining the COM of a group of atoms
- Restraint on XY Plane
- restraint potential used in the ABF calculations
- RetinalTop
- Retrieving standard deviation values while using collective variables (ABF)
- REX simulations on lonestar or ranger
- rigid molecule
- rigidTolerance question
- rmsd
- RMSD and merging trajectories
- RMSD for individual residue
- RMSD Question
- Rosetta Academic Training Webinar
- Rosetta Academic Training Workshop
- rotation question
- rotational restrains
- rough edges of energy landscape when running ABF
- run multiple walkers
- run NAMD_2.7B2
- Run simulation in NAMD using files generated by CHARMM-GUI
- Run-time system modification
- Running a simulation with a protein and a sugar
- Running a simulation with coarse-grained protein in membrane
- Running bias exchange metadynamics simulations with NAMD
- Running Charm++ over MPI does not work
- running namd faster
- running namd in parallel
- Running namd on Apple's XGrid
- running NAMD on Kraken Cray-XT4
- Running namd on Mac OS
- Running namd on multiple win32 nodes
- Running NAMD on SGI Altix system
- Running NAMD w/ CUDA under Linux
- running namd2.7 problem
- running problem
- Running problem with NAMD2.7b
- Running REMD with CHARMM f.f.
- running tcl scripting
- salt bridge
- save trajectory only for two residues
- Saving a subset of atoms
- saving psf
- Scale for Potential Bond Parameter
- scripiting problem
- script for calculation of an rmsd
- script for energy minimization of a .dcd file
- script for lipid density
- script for targeted molecular dynamics
- scripting error
- scripting problem
- scripts for starting namd with condor
- segmentation fault with AMBER topology (cvs code 03.03.2010)
- segmentation faults with AMBER topology
- Segmentation Violation: colvars
- SelectConstraints problem
- selecting potential binding cavities with MD
- Selection of alchElecLambdaStart
- selective rigidbonds
- Selectively turning off electrostatic interactions
- selectively write atom coordinates on-the-fly
- Selectively write atoms to dcd files
- Setting PME Grid
- setting transfer rate in IMD protocol
- SHAKE convergence property for CUDA and nonCUDA NAMD
- SiCortex with Pathscale
- Signal: segmentation violation
- simulating Acetylated lysine substrate complex
- simulating dna
- simulating DNA using namd::
- Simulating molecules in bulk water & VMD installation problems
- Simulating Protonated base pairs of RNA
- simulating TIP4P with NAMD 2.7b2
- simulation cell enlarging too much after restart
- Simulation configuration file not accesible
- simulation configuration file not accesible - other reasons
- Simulation crash due to charmrun error
- simulation error
- Simulation question
- simulation time instead of frames
- Simulations with NAMD
- Simultaneous FEP simulation of two distinct residues
- Simultaneous water and protein minimization
- Single or double precision?
- Single vs. Double precision
- size of integration step
- Size of Timestep
- skip frames with bigdcd
- Slab Boundary Conditions.
- Slow heating in namd
- Small discrepancy in Kinetic Energy after restarting the simulation
- SMD and langevin dynamics
- SMD and Temperature control
- SMD constant velocity pulling
- smd direction
- smd force vs time
- SMD normal vector
- SMD on membrane protein.
- SMD output
- smd output (v2.6)
- SMD output : which col represents force, second or last
- SMD restrain point in NAMD
- SMD with force applied to two seperate molecules
- SMD working only at high velocity
- soft-core FEP in namd 2.7b
- soft-core potential for FEP
- Software to Mutate DNA
- software/algorithm to cluster protein conformations
- solute movement in periodic box
- Solute moves outside of solvent box
- solution for generating IC
- solvate plugin with solvent other than water
- some problem about ABF
- some questions about smd
- some recommendations for parametrizing new molecules required
- some recommendations for parametrizing new molecules requiredþ
- something is wrong with my equilibration
- specific heat - instability
- specific site-ion LJ parameters and CHARMM general force field
- Specifying Values for Rotating Constraints
- Speeding up: Dummy constructions for aromatics or hydrogens
- spontaneous system explosion after 2 ns of normal run
- standard state correction of delta G from a PMF
- starting a job
- starting namd
- Steered Molecular Dynamics
- Steered Molecular Dynamics for more than one atom
- StepsPerCycle
- stopping protein rotation with colvars
- Strange behavior of NAMD 2.7b1
- strange error from NAMD with CUDA
- Strange vdw_dU/dl values in thermodynamic integration
- Stratification schemes
- Stray PME grid charges detected possible bug 2.7b2
- Stray PME grid charges detected: colvars
- STRIDE Structure Assignment and Ramachandran Plot Beta Strand allowed regions
- structure breaking
- structure of an equilibration script
- structure problem
- subscribe
- 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?
- switching function for electrostaic interaction
- symmetric behavior
- Symmetry in NAMD, how to achieve during a MD simulation?
- syntax error in expression "(": premature end of expression - namdstats
- system density
- System expands: CCL4 simulation; NPT(Langevin Piston)
- Take a look at jaxtr!
- targeted molecular dynamics
- TCBG "Hands-on" Workshop on Computational Biophysics, July 12-16, 2010, at San Diego
- tcl force
- Tcl forces
- tcl forces and tcl 8.5
- Tcl Forces error
- tcl forces interface
- tcl script
- tcl script for saving .coor of each frame from dcd file
- Tcl script in NAMD
- TCL: divide by zero
- TclForces and getstep
- tclforces and minimization
- tclforces included in the NAMD-FEP \delta_G values?
- tclforces: measure distances in NAMD 2.6b2 ?
- tclforces: switch from md with external forces to standard md
- temperature calculations from velocities in NAMD?
- temperature from binary velocities file
- Temperature gradient!
- Temperature rescaling vs. reassignment
- Tesla Utilization -- NAMD 2.7b1
- The accuracy of FEP calculation
- the external electric field vector
- The limit of atom number on Blue Gene/L
- the maximum numbers of atoms in NAMD?
- The MD of aquaporin in NAMD
- The outputs of REMD were suspended
- The problem of annihilating the solute in the aqueous
- the problem with NAMD2.7b
- the recent flood of unsubscribe requests
- The steps in protein and membrane simulation
- 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 ON in namd 2.7b1 compiled 24.07 when TCL forces active
- Thermodynamic integration script - where is it?
- Thiol on gold simulation in NAMD
- Timeout waiting for node-program to connect
- Timestep 594
- TIP4P
- tip4p on namd 2.7b
- TIP4P topology
- TIP4P water in AMBER parm7 format fails with 2010-06-07 nightly build
- TIP4P with NPT
- TIP4P/Ice usage in NAMD
- tmao molecule
- tmd algorithm
- TMD biasing
- TMD comments
- TMD for moving ion across membrane
- tmd log file
- TMD on tRNA does not converge
- TMD RMSD problem
- TMD SCRIPT
- TMD simulations
- to run NAMD on a PC
- Tolerance for SHAKE
- top file for CNT
- Topology and parameter file for DMF
- topology and parameter file for FAD
- topology and parameter files for guanidinium ion
- topology file for dissacharides with psfgen
- Topology files
- total charge correction
- Total energy of a residue
- trajectory in temperature from Replica Exchange MD
- Translocation problem while attempting to use ABF
- triazol parameters
- Tried to find atom type on node other than node 0
- trouble in dynamics
- trouble running metalloprotein simulation from literature
- truncated octahedral
- Tuning NAMD CUDA?
- tutorial for calculation of PMF using namd
- tutorial-l: Nanotubes tutorial - coorList(577) no such element
- two independent groups of constraints
- Two questions about essential dynamics
- Umbrella Sampling Methodology
- umbrella sampling script
- Unable to generate PSF file due to an unparametrized component
- unable to open binary file
- unbinding SMD skill question
- Unfavorable anti conformation after GLUP patching?
- Unimportant bug in output xst file writing process
- units of position coordinate velocity coordinate and timestep in .dcd and .veldcd file
- unknown path type LSN
- Unstable atoms
- Unsubscribe
- unsubscribe namd-l
- Unusual bond between residues: 0 (none) and 1 (protein)
- 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 berendsenPressure during heating
- use of tiElecLambdaStart (NAMD 2.7b1)
- use tclForce and tclBC together?
- useconstantarea
- user-defined energy function
- Using ABF to explore the conformational space of a spin label attached to a membrane protein
- Using Amber FF in NAMD
- using amber topology and parameter files in NAMD
- Using CHARMM-GUI membrane builder with NAMD
- Using NAMD for Metropolis Monte Carlo conformational searches
- Using preprotonated structure with NAMD
- Using restraints
- Using RMSD in colvar
- value 9999999.99999 during simulation
- Value for "firsttimestep" when restarting MD
- Variable results for the same simulation
- VdW and fixatoms
- VDW distance in energy minimized conformation
- VdW parameters for Zn and Fe in metalloproteins
- velocities from a DCD file
- Version 2.7 problems!
- version of namd to install
- version of tcl in binary builds
- Visit my Netlog profile
- visualize energy on a structure
- VMD-Installation problems
- vmd-l: Asymmetric water molecule
- vmd-l: display all frames simultaneously
- vmd-l: Error: failed on end of segment with RBCG
- vmd-l: GTP topology file
- vmd-l: Hardware for NAMD / VMD machine
- vmd-l: How to specify processors for running VMD on a cluster?
- vmd-l: Membrane builder ?'s
- vmd-l: namd CG minimization error: unable to find angle parameters for nxg nxx nxg
- vmd-l: namd2.7b1, tip4p, and dummies
- vmd-l: Offset for frame ids in dcd trajectory
- vmd-l: problems with CG protein-lipidbilayer-water system
- vmd-l: Restraints on coarse grained model
- vmd-l: rmsd matrix
- vmd-l: RMSD Question
- vmd-l: water molecules around proteins
- vmd-l: why atom positions are reset after readpsf, coordpdb commands?
- VMD/NAMD two identical molecules solvate in a water sphere
- 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
- Warning: Not all atoms have unique coordinates
- water "flying out of the box"
- Water Box Shape Changing during NVT Simulation!
- water box size
- Water density of water Box
- water escape
- Water is boiling with namd and charmm
- water models and some questions
- water molecules "collapse" during equilibration
- water molecules in channel protein
- Water Sphere Solvation
- water structure
- water tail correction
- water-molecules/coordenates
- waterbox changes shape during steered molecular dynamics
- Waterbox used in minimization?
- What decides the pulling direction in SMD?
- What is LINK Patch?
- what is the charge of sulfur on thiol?
- What is the different between "periodic boundary ,spherical harmonic boundary and cylindrical harmonic boundary conditions"?
- What is the Potential Energy of a Protein in Namdenergy
- where can I find the file: cornell.rtf (in bionano tutorial)
- where do I find info about freeEnergy ?
- Which compiler is used for the official (windows) NAMD binaries
- Which compiler-suite was used...
- which one is better to use - fixed atoms or constraints?
- which portions of NAMD are CUDA accelerated?
- Why do different versions of NAMD deserve different simulation results?
- Why is the temperature set different in the membrane proteins tutorial?
- Why NAMD run Slow down
- Will MPICH2 work for NAMD?
- Will MPICH2 work for NAMD? and the best way to build/compile NAMD to exploit my hardware resource?
- 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
- Would my simulation setting affect the result? About the parameter "fixedAtomsForces"
- wrapping ions
- wrapping problem
- write out the snapshot from MD trajectory
- Writing 3 subsequent timesteps to the DCD file
- writing back coordinates of waters that cross the unit cell
- Wrong energies in CUDA version
- Wtrlt: Smeart out 9/3 LJ wall
- Yet another NAMD speed concerns
- Z-direction shrinking
- Zcoord for ABF
- Zcoord-1atom for ABF
- zeroMomentum command
- zeroMomentum for SMD
Last message date: Fri Dec 31 2010 - 20:32:36 CST
Archived on: Wed Feb 29 2012 - 15:54:55 CST
4323 messages sorted by:
[ author ]
[ date ]
[ thread ]
[ attachment ]
About this archive
