NAMD-L: By Subject
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About this archive
Starting: Tue Jan 01 2008 - 09:30:16 CST
Ending: Thu Dec 31 2009 - 04:18:43 CST
- "-Wno-long-double" linking error
- "Hands-On" Workshop on Computational Biophysics, July 6-10 and August 10-14, 2009
- "within" command in NAMD?
- 'dSmooth' no longer in the ABF procedure?
- (is there) a dependence of dynamics on WRAPPING
- (no subject)
- (Á¦¸ñ ¾øÀ½)
- +1 offset to VMD index file?
- , Build your vocab (word power)-Get emails daily Fr.ee
- .inter.bin files?
- 128 core namd job fails to run
- 2 dimension PBC
- 2 molecule pair interactions
- 2 pdb files
- 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
- 2D periodic boundary condn & PME
- 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
- =20=20nodelist=20being=20ignore?= d during paralleling
- [***** SPAM *****] About APBS calculation
- [off topic] The mailing list's mailer ...
- A beginner's question for using NAMD to do cell membrane simulation and molecular transportation
- A difficult problem to explain the SMD force difference
- a question about equilibrium
- A question about restaints force.
- A script for performing calculations divided by quanta
- a timing question; 206,000atoms > 512cores not good
- A way to check for non-unique coordinates?
- ABF 'Xi' log output producing strange results
- ABF + LES
- ABF - sequence of MD runs
- ABF - using gyration
- abf and tcl scripting in NAMD
- ABF backbone dihedral
- ABF calculation - normalization of the PMF
- ABF calculation with TclForces script in the configuration file
- ABF Colvars Configuration File
- abf convergence problems
- ABF error calculation
- ABF Method
- ABF question
- ABF question (free energy partition)
- ABF simulations
- ABF tutorial
- ABF tutorial; updated FEP tutorial
- ABF using distance-com but with negative xiMin
- abf with colvars example
- ABF with different bin size
- ABF-Zcoord:
- ABF:problems with calculating Free Energy Profile
- ABF:restraint in free energy calculation in Zcoord-method
- ABF:reversibility and number of samples
- Abnormal EOF found - buffer
- Abnormal EOF found -buffer=*END*
- abnormal water surface after nvt and npt for POPC membrane
- About "Parameterizing a Novel Residue" tutorial problem
- About "Visualization and Analysis of CPMD data with VMD" tutorial
- About Amber force fields
- 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 DPD
- about force fields
- about limitdist
- About NAN error
- about psfgen
- About ref frame for rmsd vs time
- about restart
- About SMD
- about the memery lock in openMPI on infiniband
- About the namd tutorial err
- About the Nucleic Acid parameter and protein parameters
- Acceptable pressure values
- Access to CVS
- Accessing atoms and velocities during NVE run
- acridine orange
- add calcium chloride
- Add ions
- addforce on the com of a group of atoms and loadforces command
- Adding a new bond to CHARMM
- adding constraints
- adding specific forces between atoms
- adjusted background load
- advice on van Hove
- alanine dipeptide: no dihdral energy terms?
- alchemical fep amber topology
- Alchemical FEP NAMD tutorial - problems with reproducing the results
- alchemical FEP question
- alchemify with CMAP?
- AlF4
- Aligning the distance between two centroids with an axis
- Alignment of velocity dcd file
- alkane-silicon_dioxide simulation
- alpha character error in the psf file
- Amber ff99sb force-field in namd
- AMBER ff99SB on NAMD
- amber parameters for congo red
- an aptamer and a lot of stupid problems
- An outlier appear on the curve of RMSD
- angle deformation
- angle in colvars
- Another strange error: MStream checksums do not agree
- any experiences with executing parallel NAMD in a NAMD simulation
- ApoB structure
- Appending dcd when restarting a simulation
- Appending to the existing dcd file after restart
- Applying SMD to a domain of protein
- applying stress to study elasticity
- Applying weak harmonic force between two proteins
- Approach energy with SMD
- Approach energy with SMD (2)
- April promo on watches
- aromatic-aromatic interaction
- Aslos
- asphaltene parameters
- asymmetric water found!
- Asymmetric water molecule found
- Atom constraint in certain direction
- Atom velocities too high.
- atomic structure of some surfaces
- Atoms moving too fast OR constraint failure in RATTLE algorithm
- ATP and Stream files
- Automatic namd 2.7b1 installation
- autopsf and hydrogen-sites
- Autopsf error with a modified top file
- Average energy in NAMD
- Average Velocity and How to choose Right Alias
- Avoiding alpha-helix distortions
- Backbone dihedral ABF
- Background load problem
- bad exclusion error - searching remedies
- Bad global dihedral count.
- Bad global exclusion count
- base stacking analysis of the trajectory of a nucleic acids simulation
- bash: namd2: command not found
- basic question about drawing methods
- Benchmark calculation
- benchmarking of NAMD: sustained performance (TF)
- Benzene PSF
- Berendsen, explicit water
- Berendsen- two baths
- bicarbonate parameters
- binary install question
- binary trajectories
- biotin parameters and topology
- Biotin-X charmm topology
- Bond energy become Zero!!!
- bond length in terminal patches
- bonding in periodic boundary conditions
- BOUNCE namd-l@ks.uiuc.edu: Message too long (>40000 chars)
- bracket in the log file
- Bug advisory: ABF integration tool
- Bug advisory: RMSD and ABF
- bug in NAMD CVS starting March 7, now fixed
- bug or custom?
- bugfixes in the colvars module (ABF, metadynamics etc.)
- build charm++ and namd
- build missing residues in pdb
- build smp version of namd with intel 10.1
- BUILDING BPTI
- Building NAMD for Opteron Cluster with ICC
- Building Namd on a linux cluster.
- building namd on CRAY-XT3
- Building NAMD on SGI Altix
- C NH1 C minimization error
- Calcium ion binding protein
- Calcium ion-Protein Binding
- Calcium ions and psfgen
- Calculating displacement in a system with periodic boundary
- calculating energy for large log files
- calculating forces from dcd trajectory
- Calculating PMF from a constant velocity SMD simulation!
- calculation of periodic box
- can I change coordinate before restart?
- Can I get the pressure value in a cube?
- Can I use "vecnorm" in the tclforce scripts?
- Can I use another solvent rather than TI3P model in namd for MD simulations ?
- can the harmonic constraint parameters be changed between run or minimize?
- Can this be modelled in NAMD
- can we control the number and distribution of solvate molecular
- can we run EM of 2 or more proteins simultaneously
- CAN'T FIND DIHEDRAL PARAMETERS FOR CN8B CN7 ON5 HN5
- can't load forces in tclforces
- cannot find -lsrfftw... collect2: ld returned 1 exit status
- Cannot spot error in namd config file
- capping of end residues
- carbohydrates: CHARMM versus AMBER
- carma v.0.9
- catDCD 32 bit Vs. 64 bit Version
- Cell Data in DCD files - CHARMM compatibility
- cell on namd 2.7b1
- center of mass for SMD
- center of mass of dummyAtom in colvar
- center-of-mass tcl and coordinate wrapping
- CFP: 3rd Annual CMM Workshop on QM/MM Simulations
- CG bead definition
- CG equilibration recurring crashes
- CG modeling using NAMD
- CG Name Prefix Problem
- cg protein folding
- CGMD ? Hydrophobic scale
- CGMD parameters
- CGMD problem
- cgmd stability
- CGMD timestep
- change in box geometry for simulation of pure water
- change segID using segment command in psfgen
- changing dcd output file DURING run?
- changing position of atoms during NAMD simulation
- changing protonation states for a pdb with more than a single polypeptide
- Changing the atomtype of a particle on the fly
- Changing the Secondary Structure of a Protein
- Characteristic time of atomic vibrations and collisions?
- charm++ build problem
- Charm++ compilation
- Charm++ Fatal error ! Periodic cell has become too small for original patch grid!
- charm++ how to handle SMP/Multicore
- charm27 forcefield_topology
- charmm charge style
- Charmm is not free so how to learn it
- charmm parameter and topology files
- CHARMM parameters for H2S
- CHARMM to NAMD
- charmrun not found
- charmrun socket error
- Charmrun/INTEL MAC/2.7
- child models little lolita lolita sex nude preteen girls preteen pics preteen incest sun bbs underage nudist sexy preteens bbs
- Cholesterol structure
- clarification needed for wrapAll and wrapWater
- Clarification regarding some finer details in ABF simulations
- Classic timepieces replicas
- CMAP w/ D-amino acid
- Coarse grained model force fields
- Coarse grained psf file and parameter
- coarse grained simulation
- COARSE GRAINED WATER MODEL
- collective variable space PMF, including biasing potential terms?
- collective variables
- Colvars Configuration File
- colvars: Error: undefined output or restart file.
- combine PMF/dual FEP -> correct free energies?
- combining 2 dcd files into one
- combining abf reaction path
- combining segments
- compilation error "could not set locale" with intel 11.0
- compilation of the CVS code
- compilaton error
- compile NAMD 2.7b1 on Intel Xeon(R) infiniband cluster
- Compile NAMD on Bluegene
- Compile NAMD on MIPS cpu(Loongson 2F)
- compile NAMD with TCP and SMP
- compile namd2.7b1 on infiniband
- Compile Problem
- Compiling 8Core macs
- compiling charm++ failed on window with Cygwin
- compiling error of NAMD2.7b1
- compiling latest CVS on altix
- compiling NAMD failed on windows with Cygwin
- Compiling NAMD on Ranger
- compiling namd on SGI Altix
- compiling namd: cannot find -lmodulecommlib
- conf file for coarse grained simulation
- config files no longer working after software 'upgrades'
- Configurations-Statistical Mechanics
- Confira meu perfil no Facebook
- conskfile
- Constant pressure simulation: can I get the changed volume?
- Constant z axis
- Constrain centers of mass for selected atoms
- Constrain=?ISO-8859-1?Q? centers of mass for ?= selected atoms
- Constraining center of mass of monomers
- constraint energy contributions
- Constraint failure & velocity problem
- Constraint failure in RATTLE algorithm - shouldn't a rerun fail at the same step?
- constraint failure in RATTLE algorithm for atom 3205
- constraint failure problem.
- constraints
- Constraints in NAMD
- Constraints protocol
- constraintScaling - FOR LOOP
- Continuing simulation after constraint failure error?
- convergence of abf
- converting AMBER trajectory file to CHARMM trajectory file
- Converting DCD file to XTC format
- Converting PSF *BACK* to CHARMM
- COOH patch?
- coord file output minus solvation box
- Coordinate Output in both binary and ASCII. Or converting binary to ASCII in the command line
- Coordinates go to zero!
- Copper parameters for CHARMM
- Correctness of Simulation Results
- Correlation matrix of the Ca atoms
- corrupt DCD file
- Could I do the equilibration again with the same dcd file obtained?
- Could namd realizes the QM-MM method?
- Coulombic virials
- counting gas molecules inside the nanotube
- CPU USAGE
- crash with more than 96 processors (v2.7b1)
- create inositol molecule
- Creating bonds during a run
- Creating topology for carbon nanotube / any new structure
- creation and equilibration of a monolayer
- cuda 1.0 binaries on cuda 1.1
- Cuda benchmarks namd2.7b1 - effects of configuration parameters and hardware.
- 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]
- cutoffs in direct and indirect space used in PME?
- cvs logs
- cyclic peptides
- Cyclopeptide: connectivity between the first and last residues
- Cylindrical harmonic BC and constraintScaling
- DCD file format
- DCD file size
- dcd to pdb conversion
- DCOLVARS_DEBUG
- defenestrate
- defined path for NAMD2
- Defining a group of atoms in a simulation
- Defining Temperature for Langevin for Namd restart.
- Definition of two colvars for ABF
- Density Calculation
- Developing a neutral arginine patch in a topology file
- dielectric constant assignment
- dielectric parameter?
- Difference between Linux-x86_64-TCP and Linux-x86_64
- Different dcd files for minimize and MD
- Different ensembles in the same system
- Different Hbonds values on different machines using same script for same trajectories
- diffusion / fex peptide problem
- diffusion coefficient from rmsd
- Dihedral angle calculation over the trajectories
- Dihedral coordinate ABF scheme
- dihedral force constant
- dihedral restraints "on-the-fly"?
- Dihedral Restraints during MD simulation
- Dihedral scan in NAMD?
- Direction of steered molecular dynamics
- display all frames simultaneously
- DMF solvent parameters
- dmpc bilayer
- DNA pdb file
- DNA simulation by NAMD
- Do top_all27_prot_na.inp and cornell.prm share the same naming rules of atom types?
- documentation on parallel implementation
- Does amber force field in NAMD 2.7b2 work stable?
- Does anyone have a sample tcl file for counting H-bonds
- Does Berendsen increase viscosity of water?
- Does NAMD have any capability to assign coordiantes to novel sequences?
- double-wide sampling with soft-core
- Doubts and problem in ABF simulations
- drop in Temp from NVT to NVE
- dummy atom mass changed
- Dynamics with a glycerol molecule
- elastic network
- electric field along z-direction
- Electron density profile?
- Electrostatics cutoff with PME
- electrostatics NAMD vs CHARMM
- EM and MD of GPCRs
- embedding protein in membrane
- END: No log file
- Energy conversation
- Energy drif in NVE ensemble
- energy minimization
- Energy minimization failure
- energy minimization help
- Energy plot script
- entropy calculation
- Equilibration "substraction" from obtained PMF from MD
- equilibration of solvent box and pressure
- Equilibration simulation too slow.
- erergy gradient tolerance in Configuration Files
- Error : DIDN'T FIND vdW PARAMETER FOR ATOM TYPE C11
- error during heating of the minimized system: (please reply!)
- Error generating file.psf for cholesterol, missing coordinates in file.pdb.
- error in atom type
- error in explicit membrane protein simulations
- error in install NAMD_2.7b2_Linux-x86_64-CUDA
- Error in Minimization
- Error in NAMD Time Steps
- error in scripting
- error in writing restart files
- error messages with "reinitvels"
- error on installing ImageMagick
- Error on renaming file: Permission denied
- Error Parsing Config File
- error running namd
- Error running NAMD on CUDA
- Error running simulation on KRAKEN XT5
- error termination
- Error while running NPT Simulation
- Error while using NAMD
- error with calling exec: child process exited abnormally
- Error with External Electric Filed module
- Error with GUI NAMD Energy
- Error with Shape Based CG Model
- ERROR! Explicit exclusions or fluctuating charges not supported, atom ignored.
- ERROR(S) IN THE CONFIGURATION FILE when running on a cluster.
- ERROR: Constraint failure in RATTLE algorithm for atom 1880!
- ERROR: Constraint failure in RATTLE algorithm for atom 872
- ERROR: Constraint failure in RATTLE algorithm for atom 9080!
- ERROR: DIDN'T FIND "NATOM" IN PSF FILE
- Error: failed on end of segment with RBCG
- ERROR: Multiple definitions of 'LangevinPiston'
- ERROR: Stray PME grid charges detected
- Error: transport retry exceeded error
- Errors on Missing Atoms for Some Bonds
- eucb - beta testers wanted for trajectory analysis program
- Evaluating kinetic energy from a modified DCD file
- exclude 1-2
- exclude 1-2 or 1-4?
- Exclusions and CUDA
- Exiting prematurely
- Explicit Membrane Protein Simulations in NAMD/VMD
- extracting info from output files
- FAD topology and parameters of FAD
- FAD-parameters
- fail to run replica exchange on more than one node
- failure in RATTLE
- failure in RATTLE algorithm using the adaptive biasing force method
- Fatal Error Help
- Fatal error in configuration file
- FATAL ERROR: ABNORMAL EOF FOUND - buffer=*0 0 0*
- FATAL ERROR: Bad global exclusion count!
- FATAL ERROR: chdir() failed!
- FATAL ERROR: Couldn't open DCD file ubq_wb_eq.dcd: No such file or directory
- FATAL ERROR: DIDN'T FIND vdW PARAMETER FOR ATOM TYPE HN
- FATAL ERROR: DIDN'T FIND vdW PARAMETER FOR ATOM TYPE HT1
- FATAL ERROR: Duplicate bond
- FATAL ERROR: ERROR(S) IN THE CONFIGURATION FILE
- FATAL ERROR: FixedAtoms may not be enabled in a script
- FATAL ERROR: Patch needed for tuple is missing
- FATAL ERROR: Periodic cell
- 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
- Fe-S cluster topology parameters
- FEP + MCTI in one MD simulation
- FEP anomaly?
- FEP calculation of dimerization
- FEP configuration file
- FEP implementation in NAMD 2.6 vs. 2.7b1
- FEP on 2.7b1
- FEP on charged residue mutation
- FEP on NAMD2.6 versus latest CVS NAMD build
- FEP output dEavg and dG
- Fep performance
- FEP restart?
- FEP simulations?
- FEP to replace a PMF calculation?
- FEP triangular bracket average
- FEP tutorial graph question
- FEP with fixed explicit environment?
- FEP/binding free energy difference WT vs Mut
- FEP: delta_G, memory of Hamiltonians corresponding to last G value?
- FEP: FATAL ERROR: Periodic cell has become too small for original patch grid!
- FEP: How check equilibration sufficiency? calculate dG?
- filling hydrophobic cavity with... methane?
- Finer details of an ABF/colvar simulation
- firsttimestep question
- fixed atoms / pressure
- fixed atoms pdb
- fixed residue
- fixedAtoms may not be enabled in a script
- fixing parts of an equilibrated protein's environment
- fixing the protein during minimization
- flipdcd
- followup question on error calculation in ABF
- for your suggestions on Pressure Control of transmembrane protein (GPCR)
- Force Calibration Interaction
- force constant in abf configuration file
- Force Constant Units
- Force extension from SMD log file
- Force field parameters
- Force Fields
- Force on multiple atoms in ABF
- force output of pairInteraction
- force potentials for residue-based CG
- force-field for ATP
- force-field for cy3, cy5 dyes
- Forces on Atoms and Potential Energy
- Format of Binary Restart and Output Coordinate and Velocity Files
- Formating of logfile
- Free energy calculation fixing the dihedrals
- Free Energy Calculation of a protein
- free energy calculations
- Free energy of conformational change
- Free Energy of Conformational Change PMF - documentation on method?
- free enrgy calculations - an additional information
- FreeEnergy and minimization
- FreeEnergy: Not enough steps to complete pfm & mcti blocks
- fresh file not ready to read?
- from NPT to NVT
- frozen water Oxygens
- Full Electrostatic Calculations on Protein in Vacuo
- Fullerene topology
- Fwd: 99999999.9999 as vander waals energy
- Fwd: conf file for coarse grained simulation
- Fwd: convergence of abf
- Fwd: Error in Minimization
- Fwd: error in scripting
- Fwd: force constant in abf configuration file
- Fwd: How can I load two forcefied at the same time
- Fwd: Job submission to Lonestar on TACC
- 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: regarding protein-dna complex simulation please reply.......
- Fwd: RESP and CHARMM
- Fwd: Running a simulation with coarse-grained protein in membrane
- 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)
- g(r) GUI Plugin problem
- GeForce vs. Tesla
- generating psf & energy calculation for unusual amino acid - Aib
- Generating psf for NPC1
- Generating PSF from modified AMBER ff
- generating xsc and vel files
- Generation of .psf file of DNA
- Generation of average trajectory
- geomtery optimization with namd
- Getting total energy of system + pressure and temperature bath.
- 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
- GPGPU Programming summer school at University of Tennessee, Aug 10-14.
- gpu pressure control
- GPU Selection in NAMD CUDA
- Gradient tolerance nan for A three-atom simulation
- gradual increase in the temperature after minimization
- Grand canonical ensemble
- Grid Forces
- Grid Forces documentation
- GridForces methodology in NAMD 2.7b1
- Gromacs simulation not running in NAMD
- Group forces in tclForces
- GTP topology file
- H-bond occupancy in nucleic acids
- Hardware for NAMD / VMD machine
- harmonic restraint between two atoms
- Harmonic restraint parameters
- Harmonically constrained simulations
- Heat flux along CNT
- heating a system
- Help
- Help pls: Got error on FEP calculation: ERROR: The following variables are NOT VALID lambda2...
- Help reg. input file
- help regarding NAMD equilibration
- help requested
- help running NAMD energy at multiple stable temperatures (newbie)
- help with calcforces
- help with running namd-cuda for the tutorials
- help with TCL forces script
- Help: do you have the top parameter of Gla
- Hexafluoro-2-propanol (HFIP) force parameters
- hi
- Hi,all, the parameters for Strain
- Hi,Thank you!
- Histamine topology file
- hole on the surface of the waterbox
- How are the SMD atoms connected to the center of mass
- How can I calculate the distance between two atoms frame by frame?
- 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 can I monitor the force during constant velocity SMD?
- How can I set Tcouple ?
- How can I specify an exact initial velocity?
- how do you debug tcl scripts in vmd ?
- How do you evaluate forces on a fixed atom?
- How do you keep atoms a fixed distance apart?
- How does NAMD count atoms in PDB files?
- 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 analyze? Namdstats, namdplots, etc.
- How to apply an unsteady magnetic field?
- how to apply restraints for phi and psi for alpha helix regions
- How to apply velocity to the entire system with COMmotion enabled
- How to calculate free energy for conformational change
- How to choose force field?
- How to circumvent: FATAL ERROR: Periodic cell has become too small for original patch grid!
- How to compute interaction energies between individual amino acid residues
- how to config two different files for fixed atoms
- 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 fix atoms during minimization?
- How to fix relative position of a group
- How to fix the Center of mass of protein when performing SMD?
- how to generate DNA psf files?
- how to generate psf file using the AMBER topology file
- how to get 2 identical trajectories using NAMD in parallel
- How to get over with the error "Atoms moving too fast; simulation has become unstable and Exiting prematurely
- How to get over with the error "Atoms moving too fast; simulation has become unstable and Exiting prematurely.
- 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 install namd in windows xp
- how to install NAMD on suse10_ppc64 without xlc
- How to install VMD and NAMD on Ubuntu?
- How to keep Total Energy constant when an external force is added?
- How to minimize our model by SD using namd
- how to minimize the energy of a protein using CHARMM FF in 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 play molecule trajectory with VMD?
- how to prepare *.paramas file
- How to prevent cg water entering a membrane
- How to put a COM restraint on a membrane protein?
- How to read specific DCD frames directly in Fortran?
- How to read trajectory within CHARMM generated by NAMD
- How to retrieve IC50 of a specific compound from NCBI?
- How to reverse the smd pcv pulling simulation
- how to run namd in cluster
- How to run namd2 on ubuntu linux?
- how to run namd2.7b1 on multiple nodes
- How to run NVT simulations without applying periodic boundary conditions?
- how to save output file in plain text?
- how to save pdb file after "moveby" command in VMD?
- How to save the animation movie into files?
- How to save vmd figures to jpg or tiff?
- how to set initial velocity?
- How to set magnitude of cellBasisVector?
- 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 set values for cellBasisVector and PMEGridSize properly
- how to simulate a protein-ligand complex ?
- How to specify processors for running VMD on a cluster?
- How to use bigdcd on a trajectory while skipping first 1000 frames
- 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 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 to write different DCD files for separate MD runs in one simulation?
- How to write gradual heating config file
- how work: harmonic position "constraints" module + "WrapAll on"?
- HP Cluster Platform 4000
- HP-MPI on Xeon Infiniband
- HSE and gromacs
- HW - HW IN PARAMETER FILES
- Hydrogen molecule model
- hydroxyls in phosphate group collapsing
- Hydroxylysine parameters
- 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, Hostname and Port
- Implementation of graphite walls
- Implementation of TCL script in NAMD .conf file
- Implicit membrane models
- implicit solvent energy calculation
- implicit solvent model in NAMD?
- Impressive Glashutte timepieces
- impropers for aromatic residues
- Impropers in histidine residues
- inconsistence in NAMD and AMBER energy
- inconsistence in NAMD and AMBER energy: AMBER truncted octahedron
- Inconsistencies in NAMD simulations
- Incorrect Atom Count
- Incorrect Atom Count in binary file
- Incorrect PSF file for min.pme
- Increase the decimal points of energy output
- increase the temperature step by step after minimization
- Inexpensive IWC watches
- Inorganic Builder Plugin
- Inorganic compounds
- Inquire on gradual temperature increase.
- install namd on dell power edge 1900
- install NAMD on Ubuntu
- install VMD on Ubuntu
- installation of charm-6.0 in ia-64 cluster machine
- Intel 11 compilers
- Interaction energy
- Interactive protonation
- intramolecular LJ parameters
- Ionization with VMD
- ions behavior in protein-water box:
- Is it a bug? TCL Script may Lead to Overflow
- Is it better to align all the trajectory before calculating rmsd?
- is there any informatn on callback??=
- issues with AutoPSF for a cyclodextrin
- issues with AutoPSF for a cyclodextrin - addendum
- Jarzynski equality and the pull direction in SMD
- job submission script on KRAKEN @ NICS
- Job submission to Lonestar on TACC
- Kanamycin topology
- Kemp elimination substrate charmm parameters
- Keyword to start FEP calculation in NAMD 2.7b1
- Kinetic Momentum of Translation and/or Rotation
- lamboot -v nodelist
- lammps input data file
- Langevin damping coefficient
- langevin dynamics
- langevin dynamics and random seeds
- langevinDamping
- langevinHydrogen off with rigidBonds all?
- langevinHydrogen off with rigidbonds off?
- LangevinTemp and KE calculation
- Language Used and Elementary doubts
- Large MD simulations and atom number limits with NAMD
- launch NAMD from tcl script
- launch NAMD from tcl script - bug?
- LD with explicit water molecules
- Lennard-Jones potential in CHARMM
- LES problem
- ligand flies away from binding pocket
- lipid bi-layer and SiO2
- lipidmonolayer
- lithium parameters
- Load balancing off
- Loading .vel file in VMD
- loading large dcd files
- loading of large dcd files
- location of the SMD source code
- log file from 3 different protein simulations
- log file problem
- Loop
- Loops in tclForcesScript
- MacOSX 64bit binaries
- MacOSX net version segmentation fault
- Make NAMD2.7b1 with cuda bug?
- Managing Log files
- mapping of force vectors during SMD
- maximum number of devices supported per namd process
- maximum residues using AMBER parm with NAMD
- Maximum Velocities
- MD analysis
- MD for phospho-aspartate using NAMD
- MD papers
- MD performance on 10 GBit/s or 20Gbit/s infiniband
- MD problems
- MD-problems-GPCR in POPC bilayer
- Measuring protein diffusion: results too small?
- Measuring the molarity
- megatest test failure/MPI problem
- membrane
- Membrane potential
- Membrane Proteins Tutorial
- Membrane simulations
- membrane using OPLS force field
- Memory keep increasing.
- memory optimised version and exclusion check
- memory overflow problem of Tcl scripting when dealing with trajectories
- mercury ion parameters?
- merge dcd files ,catdcd
- Metadynamics in NAMD
- Methylated Histidine topology file
- mgridforce
- Mindboggling Problem Related To NAMD2 Code
- Minimisation Protocol
- minimization
- minimization and MD in one configuration file?
- minimization command
- Minimization convergence issue
- Minimization issue.
- minimization of the squared gradient
- Minimization problem of a protein-DNA complex with namd
- minimization warning and errors
- minimization with amberff
- MINIMIZER SLOWLY MOVING ATOMS WITH BAD CONTACTS DOWNHILL
- missing libraries for NAMD 2.7 on Linux cluster?
- Modeling familial amyloidotic polyneuropathy
- Modeling of Gramicidin A
- Modification of equlibrated simulation box
- Modification of equlibrated simulation box: OPTION 4
- Modification of the NAMD forcefield functions ???
- modifying a nucleobase
- Molecular dynamics of multiple organic molecules with NAMD
- molecular dynamics simulation
- molecule jumps from one site to the other?
- molefacture in vmd
- monitor a distance between two molecules
- Monte Carlo with NAMD
- mpirun compilation for NAMD
- multi-cluster configuration
- Multiple Different Harmonic Restraint Defitions
- multiple FEP experiments in one NAMD-FEP run?
- multiple simulations
- Multiple successive addforce calls
- Multiplicity of Parameters for dihedral bond exceeded
- Multiplicity of parameters for improper bonds .............. of 1 exceeded.
- mutate G->U?
- My protein went out of the water box in SMD. Would it have a bad effect on the result?
- NADP
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- NAMD & CUDA, still in development ?
- NAMD + TMD on Abe
- NAMD 1.7b1 quits writing files/hangs
- namd 2.5 compilation error
- NAMD 2.6 - PME Error on Large Protein-DNA System!
- NAMD 2.6 dcd and breaking XPLOR
- NAMD 2.6, AMD64, MVAPICH2 compile error
- NAMD 2.7
- NAMD 2.7?
- NAMD 2.7b1
- NAMD 2.7b1 ABF + free energy windows
- NAMD 2.7b1 and clustermatic
- 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 Released
- NAMD 2.7b2 with CUDA and infinband
- namd 2.7b: measure free energy difference "growing" a force constant
- NAMD and CFF forcefields
- Namd and MM-PBSA
- NAMD and multi-rail IB for improved latency
- NAMD and new sugar parameter set
- Namd benchmark problem
- NAMD binaries
- NAMD bonded energy function
- namd CG minimization error: unable to find angle parameters for nxg nxx nxg
- NAMD compilation / TACC Ranger
- NAMD COMPILATION ERROR
- NAMD compilation on linux cluster
- NAMD compile error
- NAMD crashed with TclForce turned on
- NAMD CUDA on dual Nvidia 295 GPUs
- NAMD CUDA performance degradation
- NAMD CUDA release
- NAMD CVS
- namd cvs 26.06.09, tcl 8.5, loadcoords
- namd cvs compilation
- namd cvs compilation with a maximum number of cores to run on
- NAMD CVS Installation
- namd cvs memory leak?
- NAMD CVS RUN ERROR
- NAMD disk writes and quota overflow
- NAMD documentation regarding compiling
- NAMD electrostatics no cutoff or switching
- namd energy
- namd energy self interaction reality check
- NAMD FFTW question?
- NAMD file limitation in Win32 - windows XP
- NAMD for Intel Xeon Cluster with MPICH
- NAMD hanging on GPU
- namd hangs or exits with segmentation faults on opteron cluster with infiniband
- NAMD in water vs in vacuum
- NAMD infiniband performance
- NAMD installation
- NAMD is too slow?!
- NAMD job dies on 2-quad core server
- Namd job terminates after ~10000+ itrations
- namd latest CVS version on BluegeneP
- namd linked to tcl8.5
- Namd lite
- NAMD log file analysis script problem (namdstats.tcl)
- NAMD mail bounce problem.
- namd mpi version with smp
- Namd not detecting my CUDA enabled GPU
- NAMD on 64 bit windows 2007
- NAMD on a remote UNIX and VMD on local Windows - does this work?
- NAMD on a virtual grid
- NAMD on blue gene BG/P
- NAMD on current CPUs
- NAMD on GPU
- NAMD on Ranger performance
- NAMD OUTPUT
- NAMD performance with 10GbE interconnect
- NAMD Simulation error
- NAMD stops running without error messages or termination
- NAMD Timestep
- NAMD trajectory format
- NAMD Tuning page on the wiki vs. NAMD/CUDA
- namd ubuntu-instalation
- namd vs gromacs vs charmm vs amber
- NAMD vs. CHARMM. Is complete correspondence possible?
- Namd water density
- NAMD water sphere problem
- NAMD with CUDA
- NAMD with CUDA Status ?
- NAMD with mpirun
- NAMD+MPI on AMD64
- namd-cuda-intel vs. namd-intel
- NAMD-L: autoionize error
- namd-openmosix
- NAMD-problem
- namd-SMD constant Force missing smdatom location
- namd1 - abf analysis
- namd2 erratic performance over 104 procs
- NAMD2.6 - 1D Periodic Boundary and PME - FATAL ERROR: PME requires periodic boundary conditions.
- NAMD2.6 appears to be freezing at or during load balancing
- NAMD2.6 repeatedly freezing on new desktop
- NAMD2.7 scaling problems
- 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
- namd27: tclforces activate TI calculation by default
- namd: 64 p job runs; 128 p job fails why?
- namd: ABF query
- NAMD: constraints while heating
- namd: Running namd on a node on cluster
- namd_minimize
- NAMD_ti.pl
- namdcvs
- NAMDenergy + PME for constant pressure trajectories (variable box and .xst files)
- namdenergy and amber trajectory
- namdEnergy gives significantly different values from those in log file?
- NAMDENERGY in parellel
- NAMDenergy: does rewrite temp files at different timesteps
- NAMDENERGY: function of 'cutoff' parameter when -pme option is enabled
- namdplot Unmatched " error
- need advices for running NAMD efficiently.
- Need Charmm FF for Gangliosides
- need help on CG modelling
- Need help to generate ubq-get-energy.conf
- Negative Pressure
- Neutral arginine patch in topology file.
- New open() for DCDs in v.2.6 ?
- No log file
- nodelist being ignored during paralleling
- Non Bonded Paramters
- Non-standard amino acid
- nonbonded interactions
- nonbonded potential
- nose-hoover
- NPAT - NPgT ensemble
- NPT enzemble and ABF
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- NVE ENSEMBLE
- nvidia and namd
- NVT simulation by NAMD
- NVT with truncated octahedron or with sphere?
- NVT/NPT pressures w fixed particles
- Offset for frame ids in dcd trajectory
- Oligomer
- on NAMD simulation of DNA translocation through nanopores
- On naming rules in force-field parameter files?
- one atom off in the minimization result
- OPLS-AA toppar files
- Optimizing configuration option for fast calculations
- order parameter, lipid segments as vectors
- output .coor minus solvation box
- output area
- Output force acting on each atom in the system
- Output of forces.
- output while tclforces active
- outputname and restartname
- OXT in pdb file
- pair interaction
- Pair interaction : Energy values are zero
- Pair Interaction Calculations to get Charmm Charges?
- Pair interaction runtime analysis skipping dcd frames
- pairlist i_upper mismatch!
- palmytoilated
- Par and Top files for BCL
- par-extraterms.inp file needed
- parallel execution speedup
- Parallel TMD (2.7b) dies : "MPICH internal error"
- Parallelism issue
- PARAM22 and CMAP correction
- paramater about Amphotericin B
- parameter file to make cholesterol psf file
- parameter for compiling
- parameters and topology file needed for coarse-grain simulation
- Parameters for esters
- Parametrizing a novel residue
- paramter
- Paratool: where is "tip3.xbgf"?
- patch DISU to 2 residues
- patch LINK - cyclizing a protein
- pbc
- 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
- Periodic BCs
- Periodic boundary condition in a membrane simulation
- periodic boundary conditions
- Periodic boundary conditions in membrane simulation
- Periodic Box Size vs. Water Box Size
- periodic cell conditions for membrane simulation
- Periodic cell has become too small
- periodic cell has become too small for original patch grid!
- Periodic Forcing Functions
- phi and psi restraints for 2 helix regions
- phosphate (PO4) topology
- phosphohistidine parameters ???
- phosphoserine simulation using toppar files and NAMD
- Platinum paramaters
- Please disregard the spam "Lei sent you private photos on Tagged :)"
- Please unsubscribe me
- PLUMED release 1.0.0 available
- PLUMED release 1.1.0 available
- PME and fixed atoms questions
- PME and infinite polymer
- PME and r-RESPA issue in NAMD
- PME fails no matter what
- PME Grid Size - how far to deviate from cell basis vectors.
- PME non-zero charge
- PME questions
- PMEGridSize
- PMEGridSpacing
- PMF calculation floating-point error
- PMF via constrained dynamics in NAMD
- PMF: free energy calcs in "grow" phase?
- POLL: free energy of conformational change
- polymer topology file
- Postdoc position in biomolecular simulation
- Postdoc position in computational biophysics and nanotechnology
- Postdoctoral Position in Scientific Computing
- Precision of Coordinate data
- pressure calculation
- Pressure coupling and system heating
- Pressure oscillation in NPT
- pressure profile
- pressure profile calculations
- Pressure related issue
- PRESSURE, GPRESSURE, PRESSAVG, and GPRESSAVG
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- problem about NAMD compile
- problem compiling NAMD2.6 in a MacOSX-PPC
- Problem generating psf file in psfgen
- Problem in energy conservation in NVE ensemble with 1fs timestep
- problem in fitting Maxwell-Boltzmann distribution
- Problem in making cyclic peptide
- problem in NAMD minimized structure when viewed in VMD ramaplot
- problem in solvating the protein
- Problem namd2 and mpich2
- problem namd2-MPICH
- Problem regarding psfgen
- Problem running NAMD on ranger@TACC
- Problem to generate water segments and lipid reading in membrane
- Problem while installing NAMD
- Problem with .conf file of NAMD
- Problem with creating psf file from structure made by inorganic builder
- problem with executing MPI program in NAMD simulation
- Problem with NAMD crashing without warning or error messages
- Problem with number of steps > 1000000
- Problem with TclBC when run in more than one processor
- Problem with temperature increase in equilibration.
- problem with VMD installation- libstdc++.so.5 => not found
- problems compiling charm and NAMD on intel cluster using MPI over ethernet
- Problems compiling NAMD
- Problems deciphering fepout
- Problems found --- [Fwd: Bad global dihedral count.]
- problems of "Stray PME grid charges"
- Problems on SMD simulation
- Problems restarting an amber simulation
- problems sourcing namdstats in vmd
- problems with CG protein-lipidbilayer-water system
- problems with combine.tcl
- Problems with CUDA Build
- Problems with minimization
- Problems with OPLS in NAMD
- Problems with the charge (membrane simulation)
- Problems with TMD could not be solved with the CVS version
- problems-periodic cell
- problems-protein minimization
- processor counts FFT and NAMD
- protein collapsing problem
- protein collapsing problem!
- Protein collpasing problem!
- protein folding
- protein folding cg
- protein instability
- Protein moving out of water-box after 10 ns simulation
- protein shifts out of the water box
- PROTEIN VACUUM MINIMIZATION ERROR
- protein_RNA simulation
- Proteine-membrane simulation.
- protocol to start MD
- Protonation of nucleic acid phosphates in CHARMM for use in NAMD
- PSF file
- psf file creation
- psf gen
- psf generation for a small non-peptide molecule
- psf generation for a small non-peptide molecule - again
- PSF of Tryptophane methyl ester
- psf-generation.
- PSF/top/inp for joint charmm/amber benchmark
- PSFGEN
- psfgen fails to set coords for all atoms
- PSFGEN Warnings about H positions on standard amino acids
- psfgen: more problem
- psgfen patch
- ptraj --- 2drms
- puase MD integration to communicate between jobs
- Pulling atoms in different directions
- python vs tcl
- Quantitative Test for Equilibration of Data Time Series
- quartz / FF(Lopez&MacKerrel)
- quartz slab / pairInteractionSelf / Bad global exclusion count!
- Query Regarding FEP tutorial: NPT or NVT?
- Question about 'NAMD TUTORIAL'
- Question about a shift in rmsd using fixedatom off
- Question about catdcd and DCDunitcell
- question about cellBasisVector*?
- Question about Error Message
- question about FEP soft-core
- question about repeating output text
- question on ABF
- question on forces / theory
- Question on mutator in VMD
- Question regarding ABF simulations
- question related to rmsd
- Questions about equilibration
- Questions concerning 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
- RAM/node
- RAMD in NAMD
- RAMD in NAMD; bugs and new version 4.0
- Random Expulsion MD (REMD)
- RBCG tutorial
- Re- Loading .vel file in VMD
- Re-posting - Methylated Histidine topology file
- Read dcd file and calculate (distance/constraint energy Vs snapshots) using NAMD
- Read DCD file in Java
- Reading and writing Binary Restart or Output files with Fortran
- Reading multiple .log files
- Reading multiple .log files into one
- Reassign temp
- Reassign Temp during the Production Run
- reassignFreq script
- recalculating energy using dcd file
- recent papers on MD gotchas with PRNG seeds
- recenter atom and remove rotation (translation)
- Reference file for the constraining force in Umbrella Sampling
- reference of ewald method
- reg dynamics
- reg parameter of ions
- Regarding ABF Simulation
- Regarding amber parameters using NAMD
- regarding cgmd
- regarding implicit solvent models
- Regarding Installation
- Regarding Lipid Order Parameter Calculation
- Regarding NAMD CPU usage
- regarding positioning of protein molecule
- regarding protein-dna complex simulation
- regarding protein-dna complex simulation please reply.......
- regarding protein-protein interaction
- regarding psfgen algorithm
- Regarding REMD
- regarding simulation
- regarding topology file generation
- regarding writemol2
- Regd :parameter file
- Regd: Error
- regd: my parameter file
- relating to NAMD Energy Plugin scripting
- REMD
- REMD on AIX5.3
- removing water from big dcd files
- Replay to Parametrizing a novel residue]
- Replica Exchange Method
- Replica Exhange error: POSIX EINTR {interrupted system call}
- Replica or Original?
- Replica Server Tutorial
- Request for information regarding ABF in NAMD.
- Rescale Temperature when velocity of COM is not zero
- RescaleFreq of temperature =1?
- resonable dcdfreq
- restart
- restart PMF calculation: what is "lambdaRef" output?
- restart PMF: grow phase required? "lambdaRef"? more documentation on NAMD PMF?
- restart REMD simulation
- restart_minimization
- restartfreq question....
- restarting a simulation
- Restarting a Simulation & Langevin
- Restarting ABF
- restarting ABF simulation
- restarting calc giving new temperatures
- restarting files converge to new temperature
- restarting heating protocol problem:
- restarting issue
- Restarting simulation goes the different temperature
- restating simuation and periodic cell conditions
- restraining the COM of a group of atoms
- restraint on a group of atoms at their center of mass?
- Restraint Potential
- Retrieving standard deviation values while using collective variables (ABF)
- reversing constant velocity SMD
- REX simulations on lonestar or ranger
- Re£ºHow to fix atoms during minimization?
- right_protocal
- Rigid body effect, translational kinetic momentum
- rigid body model
- Rigid bonds and hydrogen bonds "on" inaccurate/invalid?
- rigidTolerance question
- Rise in Total Energy in NVE
- rms gradient
- RMSD and merging trajectories
- RMSD for individual residue
- rmsd_RNA_DNA
- RNA_minimization
- Rosetta Academic Training Webinar
- Rosetta Academic Training Workshop
- Run NPT ensemble simulation with sphericalBC?
- Running a simulation with a protein and a sugar
- Running a simulation with coarse-grained protein in membrane
- Running CGMD using NAMD
- Running Charm++ over MPI does not work
- Running minimization, heating and FEP simulation within the same configuration file.
- Running Multiple TMD simultaneously
- Running NAMD at TACC (Ranger)
- running namd in parallel
- running namd on cluster
- running NAMD on Kraken Cray-XT4
- Running NAMD w/ CUDA under Linux
- running namd with condor
- running NAMD with ranger@tacc
- running namd2.7 problem
- running precompiled NAMD with multiple processors
- running problem
- Rv: Value 99999999.9999 during minimization
- S-OXY CYSTEINE parameter
- Saving a subset of atoms
- scalability problem on linux cluster
- Scale for Potential Bond Parameter
- scaling the interaction energy
- scripiting problem
- scripts for starting namd with condor
- Seeking suggestions to decide on realistic configuration values
- segmentation fault when running ABF
- segmentation fault when running ABF]
- segmentation fault?
- Segmentation Violation: colvars
- SelectConstraints problem
- Selectively turning off electrostatic interactions
- selectively write atom coordinates on-the-fly
- Selectively write atoms to dcd files
- Setting PME Grid
- Shear flow: Lees-Edwards Boundary Conditions
- SiCortex with Pathscale
- Signal: segmentation violation
- Simple query
- Simulating molecules in bulk water & VMD installation problems
- Simulating Protonated base pairs of RNA
- simulation configuration file not accesible - other reasons
- Simulation crash due to charmrun error
- Simulation issues: water box deformation after minimization and shifting protein coordinates during production run
- Simulation of Thiolated Biotin-Streptavidin on Gold
- Simulation stalled at startup
- Simulation with non-periodic boundary condition
- Simultaneous water and protein minimization
- Single or double precision?
- Single topology FEP
- Single vs. Double precision
- size of integration step
- skip frames with bigdcd
- Slow heating in namd
- Small discrepancy in Kinetic Energy after restarting the simulation
- SMD and Temperature control
- smd direction
- SMD force units
- smd force vs time
- SMD forces
- SMD in water
- SMD more than once
- 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 vs RAMD
- SMD vs RAMD / TMD
- SMD with force applied to two seperate molecules
- SMD working only at high velocity
- SMD-Applied Forces and Analysis
- Soft core potential - tested or not?
- soft-core FEP in namd 2.7b
- soft-core potential for FEP
- Software to Mutate DNA
- solution for generating IC
- solvate a molecule
- solvate plugin with solvent other than water
- solvate replicates water box (2 by 2 by 2) and segments (8X) for no apparent reason
- solvate using Helmut Grubmuller's SOLVATE and then VMD, then how to minimize properly!
- solvating protein
- some problem about ABF
- Some question about Target MD
- some recommendations for parametrizing new molecules required
- some recommendations for parametrizing new molecules requiredþ
- spawn_namd_command How to properly execute this command
- Speeding up: Dummy constructions for aromatics or hydrogens
- spermine force field
- spontaneous system explosion after 2 ns of normal run
- srand in a tclforces script
- steepest descent technique
- Steered Molecular Dynamics
- Steered Molecular Dynamics for more than one atom
- stopping protein rotation with colvars
- storing velocity data of a NVE simulation
- strange error from NAMD with CUDA
- Strange Input Error
- Stratification schemes
- Stray PME grid charges detected: colvars
- structure problem
- Struggling with the compilation of NAMD 2.6 on a PBS Cluster with LAM/MPI
- Stupid question about compiling NAMD with cygwin on windows
- submit namd job in cluster
- subscribe
- subscribe namd-l
- Sudden expansion of box when continuing NPT simulation
- swig wrapping c++ code on nersc
- symmetric behavior
- syntax error in expression "(": premature end of expression - namdstats
- System expands: CCL4 simulation; NPT(Langevin Piston)
- Take a look at jaxtr!
- TARGETED MD - GRADUAL INCREASE OF FORCE
- TARGETED MD ERROR
- Tcl "loadtotalforces" question (forces never seem to be saved)
- tcl force
- Tcl forces
- TCL Forces : OUT OF MEMORY
- tcl forces interface
- tcl forces/membranes
- tcl script
- TCL/NAMD: FATAL ERROR: error reading output from command: interrupted system call
- TCL8.5? or
- TCL: divide by zero
- TclBC - multiple iteration
- tclforce script in FEP: global variable
- TclForces
- TclForces and getstep
- tclforces and minimization
- TclForces and wrapping
- tclforces included in the NAMD-FEP \delta_G values?
- tclforces: switch from md with external forces to standard md
- temperature calculations from velocities in NAMD?
- temperature from binary velocities file
- Temperature rescaling and reassignment parameters
- Temperature rescaling vs. reassignment
- temperature stepping during heating
- Tesla Utilization -- NAMD 2.7b1
- Tests not running for Charm++ Myrinet with MPICH-MX
- Thank you for your advices
- The correct topology/parameter file and pgn
- The correlation of SMD force vs. AFM data
- the external electric field vector
- The limit of atom number on Blue Gene/L
- The MD of aquaporin in NAMD
- the recent flood of unsubscribe requests
- The steps in protein and membrane simulation
- 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
- Time factor
- Time Step is Incompatible in the NAMD DCD Analyzed with CHARMM
- Time step is incompatible in the NAMD DCD file analyzed with CHARMM
- TIP4 water model NAMD
- TIP4P
- tip4p on namd 2.7b
- TIP4P topology
- tmao molecule
- TMD + harmonic restraints
- TMD + temperature/pressure coupling
- tmd algorithm
- TMD AND RIGIDBONDS
- TMD and TclForces
- TMD biasing
- TMD bug correction???
- TMD comments
- TMD for moving ion across membrane
- TMD on tRNA does not converge
- TMD RMSD problem
- TMD SCRIPT
- TMD SIMULATION - RMSD DOUBT
- To channel bond or not ?
- To incorporate an energy term
- to run NAMD on a PC
- Tolerance for SHAKE
- top_all22_model.inp
- Topology and parameter file for DMF
- topology and parameter file for FAD
- topology and parameter files for guanidinium ion
- Topology cartoon of proteins
- topology file for 2 sugar rings connected 1-1 between them
- topology files
- topology/parameter entries for asphaltenes?
- topology/parameter entries for methane?
- topology/parameter file for ligands
- torsion potentials for phi/psi angles in CHARMM force field?
- Total energy of a residue
- tracing not available with CMK_OPTIMIZE!
- trajectories
- Trajectory file formats & structural alignment
- Translocation problem while attempting to use ABF
- triazol parameters
- Tried to find atom type on node other than node 0
- trifluoroethanol (TFE) solvent
- Trouble in energy minimization with warning to increase cutoff
- Trouble with params file when trying to perform basic dynamics with alanine.
- truncated octahedral
- Truncated Octahedron for VMD and NAMD simulation
- Tuning NAMD CUDA?
- Turn off H-bonding on select residues
- tutorial for calculation of PMF using namd
- two independent groups of constraints
- Two questions about free dynamics simulation
- TXT program editor
- Typical maximization steps
- ubuntu reads my psf as an audio file
- umbrella sampling of decalanine using the ABF module
- umbrella sampling script
- Unable to edit files in NAMD folder.
- Unable to generate PSF file due to an unparametrized component
- unbinding SMD skill question
- underage russian lolita preteen lolita lolita preteen nude preteen models young preteens underage lolita preteen girls nude kids nymphets
- Unfavorable anti conformation after GLUP patching?
- Unimportant bug in output xst file writing process
- unknown path type LSN
- unknown residue LIP
- unsubscribe
- unsubscribe namd-l
- unsubscribe-namd
- Unsure about current setting of Periodic Boundary Conditions
- Unusual bond between residues: 0 (none) and 1 (protein)
- unwanted bonds in .pdb file while using molefacture
- use of 'measure hbonds'
- use of berendsenPressure during heating
- use of charmm27 & NPT ensemble for lipid bilayer simulation
- use of tiElecLambdaStart (NAMD 2.7b1)
- use tclForce and tclBC together?
- Use tclforces to find systematic forces on fixed atoms?
- useconstantarea
- useGroupPressure with no RigidBonds ?
- Using Amber FF in NAMD
- using Amber paramter
- using amber topology and parameter files in NAMD
- Using NAMD to calculate pair energy with many subset permutations
- Using preprotonated structure with NAMD
- Using restraints
- value 9999999.99999 during simulation
- Value 99999999.9999 during minimization
- Value for "firsttimestep" when restarting MD
- van der walls-understanding problem
- Variable results for the same simulation
- variation between results on different OSes
- VDW distance in energy minimized conformation
- vdW parameter
- velocities
- velocity DCD data retrieval
- Velocity scaling and thermostatting both at a time
- velocity units in .vel file
- virtual and heavy hydrogens in NAMD
- Visit my Netlog profile
- visualize energy on a structure
- VMD-Installation problems
- vmd-l: C NH1 C minimization error
- vmd-l: CG bead definition
- vmd-l: counting gas molecules inside the nanotube
- vmd-l: display all frames simultaneously
- vmd-l: Error: failed on end of segment with RBCG
- vmd-l: Fwd: memory overflow problem of Tcl scripting when dealing with trajectories(sorry for cross mailing...)
- vmd-l: GTP topology file
- vmd-l: Hardware for NAMD / VMD machine
- vmd-l: How to generate more segments?
- vmd-l: How to read specific DCD frames directly in Fortran?
- vmd-l: How to specify processors for running VMD on a cluster?
- vmd-l: Loading .vel file in VMD
- 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: TAB key in vmd terminal
- vmd-l: TXT program editor
- VMD-NAMD-commands
- VMD/NAMD two identical molecules solvate in a water sphere
- Warning in log file
- Warning: Not all atoms have unique coordinates
- water box getting deformed
- water box size
- Water density of water Box
- Water is boiling with namd and charmm
- water models and some questions
- water models supported in NAMD
- water molecules "collapse" during equilibration
- water molecules in channel protein
- Water Sphere Solvation
- water tail correction
- Waterbox unexpectedly deformed after minimization.
- WCA Particle
- What decides the pulling direction in SMD?
- What does "cellOrigin" really mean?
- 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 unit of coupling coefficient when using tCouple to control temperatue?
- where can I find the file: cornell.rtf (in bionano tutorial)
- Which compiler-suite was used...
- Which conformation is more proper for the SMD
- Which namd on amd64?
- which portions of NAMD are CUDA accelerated?
- Why is the temperature set different in the membrane proteins tutorial?
- Why there is a bond between the two Hydrogens of the TIP3P water in Amber force field?
- Why turning on 'pressureProfile' make NAMD get into sleep?
- Will MPICH2 work for NAMD?
- Will MPICH2 work for NAMD? and the best way to build/compile NAMD to exploit my hardware resource?
- won't launch on linux ubuntu cluster for a parallel run
- Would my simulation setting affect the result? About the parameter "fixedAtomsForces"
- Wrap ions?
- Writing 3 subsequent timesteps to the DCD file
- Wtrlt: Smeart out 9/3 LJ wall
- xsc file format
- Yet another NAMD speed concerns
- zeroMomentum command
- ZINC parameter
- Zinc-NAMD parameters
Last message date: Thu Dec 31 2009 - 04:18:43 CST
Archived on: Wed Feb 29 2012 - 15:51:50 CST
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