NAMD-L: By Subject
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About this archive
Starting: Mon Jan 02 2006 - 18:54:15 CST
Ending: Thu Dec 27 2007 - 12:55:11 CST
- "Adaptive" force direction in SMD?
- "atoms moving too fast" error in bilayer simulation
- "binaryoutput no" doesn't work
- "CWeb performance data sent to wrong processor..."
- "measure" command
- "Not all atoms have unique coordinates"
- "reinitvel" parameter in config file
- "RESTARTING CONJUGATE GRADIENT ALGORITHM"
- "Timeout waiting for node-program to connect" error, only sometimes
- "Unknown pragma ivdep and pragma vector" errors when compiling on BlueGene
- "wrapAll on" with a complex
- #QNAN: Please help!
- (no subject)
- *** topology file for AMP? ***
- *.dcd and *.dcd.BAK
- ------------- Processor 0 Exiting: Called CmiAbort ------------
- .xsc file and .restart.xsc file
- 0 coordinates for LES atoms in pdb file after solvation
- 128+ proccessor jobs on 64bit Widows hang upon completion of the simulation.
- 2 proteins
- 2-D periodic boundary condition
- 2D Ewald summation
- 64 bit NAMD on AIX and CatDCD
- <no subject>
- =20=20How=20to=20compile=20NAMD?= 2.6 on core2 operons, x86_64-redhat-linux,which isqthe=20proper=20choice=20in=20Arch.?=
- =20?= qHow=20to=20compile=20NAMD2.6=20on=20core2=20operons,=20x86=5F?= 64-redhat-linux,which is the proper choice in Arch .?=
- =20?= qhow=20to=20constrain=20a=20dihedral=20angle=3F?=
- =20How=20to=20build=20charm++=20on=20c?= ore2 processor
- [Fwd: HD speed ??]
- [Fwd: increasing RMSD after 2 ns minimization-equilibration]
- [Fwd: SMD of titin domain]
- [Fwd: Specific Heat Calculation with VMD]
- _NAMD_crashes?= on winx64 during parallel run.
- a basic question
- A basic question?
- a display problem
- a error during install charm-5.9
- a name quesiton
- a philosophical question...
- A possibel wrong coding in Parameters::read_charmm_parameter_file(char *)
- A puzzling problem about adsorption energy in solution.
- A question on simulation with NPT ensemble
- A serious problem of NAMD output.
- A strange phenomenon in my dynamics system,any suggestion?
- a topology file in VMD
- abf "force not a vector" error
- ABF (fwd)
- ABF - changing the reaction coordinate
- ABF - PMF Calculation
- ABF - restricting reaction coordinate
- ABF - stretching deca-alanine
- ABF - zCoord for more than one monomer
- abf - zeros as output
- ABF : dihedral-com.tcl
- ABF application
- ABF calculations
- ABF fullsamples
- ABF inFiles
- ABF on a single molecule
- ABF or SMD
- abf output
- ABF Output File
- ABF parameters
- ABF question
- ABF restrain
- ABF Simulation
- ABF with z-coord
- ABF: example works now; more questions.
- ABF: example works; more questions.
- abf: multiple distance
- ABF: split reaction coordinate in widows
- About "get z" command in MD script language.
- About "mutate" command in psfgen package.
- about 'loadforces' command...help!
- about abf
- About CHARMM charge
- about counterions
- About cutoff parameter for real space calculation in PME
- about diahedra entry in top_all22_sugar.inp
- About Langevin Damping Coefficient.
- About Langevin Dynamics.
- About loadcoors -- is there a loadvelocity?
- about normal mode analisys
- About para file format
- About pmf
- about PMF and MCTI
- About pressureProfile command for non-equilibrium system.
- About QM-MM
- About restart.vel.old file.
- About RMSD
- about signal 11 received,exiting
- About smd
- about TCL boundary forces
- About the command "set z [lindex $coorList($i) 2]".
- About the error of "Tcl interface"
- About the module of "External Electric Field "
- about the MSE residue
- About the unit of "efield"
- About timestep again.
- About timestep again. -- Fastest motion O-H streching period 10 fs.
- about topology generation
- abrupt deviation in rmsd values
- Accelerating groups of atoms
- Accepted temperature and pressure oscillation
- ACE patch
- Acetaldehyde Dihedral Parameters
- AcetylProlineAmide topology
- across the nodes, namd jobs don't get enough CPU!
- add Mg2+
- addforce
- adding extra ions to neutralize charge on protein
- affecting the atom velocities
- Alchemical Free Energy Perturbation
- Alchemical Free Energy Perturbation Simulation
- alchemical transformation
- aligning ligands
- Aligning structures
- all atom simulations with explicit water molecules and langevin thermostat
- all atom simulations with explicit water molecules and langevinthermostat
- Altix Performance Tuning
- Altix performances
- Amber Parameter in NAMD
- Amber PARM Input File Example?
- amidated C-terminus (NH2) with OPLS force field
- Angle 2, Where is the problem [IMPORTANT]
- Angle CO2 Problem
- Angles and dihedral generation
- ANN: MDAnalysis 0.3 python library
- ANN: MDAnalysis python library
- Announcement: QM/MM Workshop
- Another question on Diffusion
- Any flag values returned when executing "minimize" and "run"?
- any SD minimization in NAMD?
- Anyone have catdcd-4.0 for BlueGene?
- apply force along an internally defined direction
- apply periodic boundary condition in one direction
- Applying conformational constraints during simulation
- applying experimental constraints to a MD simulation
- area per lipid for a protein embedded membrane system
- Area per lipid.
- assigning atom type for parameterization
- Asymmetric water molecule found???
- Atom distance & ptraj
- atom distances
- atom name based paremeters
- atom restraints
- atom type HZ4 not found
- Atomic partial charge
- atomlist command in matdcd
- Atoms mooving too fast ... still the problem
- atoms moving fast
- Atoms moving too fast error
- ATP molecule
- attractive harmonic potential between 2 molecules
- autocorrelation function !
- AutoIMD
- Autoionize error: spontaneously quits
- autoionize plugin..
- Autopsf
- Avoiding self-interaction with PME.
- bad exclusion count
- bad global exclusion count error
- bad global exclusion count in LES
- balck box: what is the coupling constant when using langenvinFile?
- barostats in NAMD
- basic pdb file run with namd and vmd
- Basic question about steered moledular dynamic(SMD) simulation
- Basic question.
- Benzamidine parameters
- Berendsen pressure control problem
- Best NAMD version for Rocks 4.3 IBM xseries 3665
- BigDCD
- bilayer thickness in simulation of POPC membranes
- Binary for MacOSX-i686
- binary.coor to ascII.coor
- binaryoutput option doesn't work for dcd file
- Binding Free Energy
- Binding free energy by LIE
- biotin charmm topology/parameters
- Bizarre atom behavior
- Boiling temperature of water.
- Box size
- Buffering problems while attempting to read log file
- bug in pressure calculation with E field?
- build script in charm++-5.9 does not find mpicc or mpicxx for mpi-linux version
- Building 64-bit NAMD
- Building a pdb file
- Building Charm .. mpi-linux-amd64-ifort/tmp/traceCore.h .. and .. mpi-linux-amd64-ifort/tmp/MsgPacker.h
- Building cluster
- Building for SunGrid
- Building molecule from topology file
- Building NAMD 64-bit Mac OSX with GCC
- Building NAMD with Myrinet MX
- Building NAMD/CHARM++ Mac OS X Intel
- Building PDB files for DNA.
- bulid psf for structure already with hydrogens
- bulk density in RDF.tcl
- bunch of water molecules
- C1 splitting documentation
- C:CA bond getting stretched
- calculate interaction energies for a system with amber forcefield
- calculate potential energy from DCD file
- Calculating macroscopic properties
- Calculating or Outputing Forces
- calculation (continue)
- Calculation of CHARMM Parameters from GAMESS Output.
- calculation of non-bonded interactions
- Can any one help me with this parallel issue
- Can I do ¡°accelerated molecular dynamics¡±in NAMD?
- can i somehow use reassigntemp for selected atoms only?
- Can I use FEP in NAMD for reaction of ATP with Kinase?
- Can I use namd for carbon nanotubes?
- Can NAMD be used as for general Newtonian mechanics simulations?
- Can NAMD perform random expulsion molecular dynamics(REMD)?
- Can NAMD perform random expulsion moleculardynamics(REMD)?
- can someone comment?
- Can someone PLEASE explain the "firsttimestep" parameter ?
- Can you imagine?
- Can you satisfy your girlfriend?
- Can't find a good drug store?
- Can't stand sex all night long?
- Cannot open file 'pair.pdb'
- Cannot specify both an initial temperature and a velocity file
- Can´t use charmm to perform dcd analysis
- caps
- Cell membranes with lipids different from POPC and POPE
- CellBasisVector
- centre of mass fixed
- chage free energy
- Cham++ errors
- change center of spherical BC during sim
- change in Disulphide Patches
- Changes to dihedral angles
- Changing loop to helix: restraining about 20 dihedral angles
- changing parameter files during simulation run
- Changing the protonation states of residues
- changing velocity during simulation
- charge on protein
- Charged Atoms in External Magnetic Field
- Charges in NAMD topology file
- charges in topology
- Charm compile: "xlC: command not found"
- charm installation problem
- Charm++ Compilation
- charm++ over MPI
- Charmm 22 vs Charmm 27
- charmm charge style
- CHARMM forcefield is free?
- Charmm format topology and parameter files for FAD
- CHARMM partial charges and paratool
- charmm str file
- Charmm to Namd!!
- CHARMM top and par files for PO4
- charmm toppology : internal coordinates
- charmrun + NAMD on dual quad-core intel procs
- Charmrun and ssh problem
- Charmrun issues and namd on Win 64
- charmrun simulations over macpros
- CHARMRUN vs MPI
- charmrun: execve failed to start; intel dual core Redhat
- checkpoint / revert
- checkpoint software for NAMD?
- cis/trans prolyl
- cluster / scratch space
- clustering conformations
- Clustering of conformation
- clustermatic 4
- Clustermatic and NFS mount
- CMAP
- CMAP and NAMD
- CMAP in NAMD simulation
- CMAP in NAMD?
- CMAP problem
- CNT modeling
- Coarse-grained Modeling/User defined FF
- Code question: Partitioning the patch contents into water and non-water
- collision correction of Locally Enhanced Sampling
- COM restraint in NAMD
- combine pdb files
- combine.tcl
- combined QM/MM calculation with NAMD
- command line arguments in NAMD ?
- Comments on 'restart' simulation
- compilation of charm++
- Compilation of Charm++ then NAMD 2.6 on Opteron with Portland compilers
- Compilation of Charm++ then NAMD 2.6 on Opteron with Portlandcompilers
- Compilation on IBM-Power (Linux)
- Compilation problems on intel woodcrest
- Compile charm++ with icc
- compile error on amd64 in src/ComputeTclBC.C
- Compile NAMD on Bluegene
- compile NAMD on Intel-64
- compile NAMD/CHARM on infiniband cluster
- Compiled NAMD on SGI Altix
- compiling charm++ with g++ 4.1
- compiling namd
- Compiling NAMD 2.6 from Source: no charm-5.9.tar
- compiling namd intel 9.1
- Compiling NAMD on AMD64 dual core
- compiling NAMD on an elan-linux-ia64 arch
- Compiling namd on ibm-power + red hat linux
- Compiling NAMD on PPC G4 w/Apple's Leopard
- compiling namd2
- Compiling Questions
- Complete Beginner
- compute nonbonding interactions on bonded atoms
- computer network
- Computing cost of frozen atoms
- Computing Potential of Mean Force --SMD-cv
- Configuration file
- Configurational temperature - coordinates
- const vel SMD
- Constant electric field to selected atoms.
- Constant Energy Simulations
- constant velocity SMD
- Constrain EVERY bond length and bond angle
- Constrain only in Z direction
- constrained simulation
- Constraining a molecule and measuring the corresponding constraint force
- Constraining angles ??
- constraining distance
- constraining water so that it does not get inside bilayer
- constraints on zinc ions
- Constructing a small molecule
- constructing a topology entry for hexadecane
- Continue a run ?
- COntraints for lipid bilayer simulation
- Controlling the area per lipid
- convergence monitoring...
- Convergence of ABF calculation: n_samples
- Conversion for forces
- Conversion of .dcd into .xtc format
- convert .dcd into .trr
- Converting a PSF file from one forcefield top another
- CoordinateTransformation
- coordination chemistry with NAMD
- Copper and Zinc: top_all27_prot_lipid.inp
- Correlation Functions
- corrupt dcd file >2GB on PowerPc
- Count protein solvent HBs?
- Counting H-bonds from a dcd file
- Crazy defoliator
- Creating PDB from PSF and COOR files
- Creating topology for carbon nanotube / any new structure
- Crystal Structure Analysis
- cubic periodic boundary box: what happen if I use a rectangular box?
- custom pulling path
- Data from Output file
- data structure of neighbor list
- dcd binary file format
- DCD file
- dcd file format
- dcd file is too large
- dcd file produced with NAMD can be used with AMBER?
- DCD file really corrupt?
- DCD for windows
- DCD to PDB conversion
- DCD trajectories produced by SMD simulation
- dcd trajectory format
- deformations in a cubic water box during equilibration in NAMD
- deformations in a water box during equilibration in NAMD
- Deformations under constant strain rates
- deformed water box after heating
- deformed water box during equilibration.
- DEN residue name in Amber
- Density of water
- density of water molecules in a water sphere
- deprotonated form of Proline molecule
- Determining Equillibration of a membrane protein
- Determining Transition State from an Unfolding Simulation
- Developing topologies for modified NA residues?
- Did anybody really use TIP4P?
- difference between reassignfreq and rescalefreq in temperature controls.
- difference in total energy values
- Differences between 32bit and 64bit version of NAMD?
- different 1-4scaling values for different atom types?
- different cutoff for elecstrostatic and VDW interactions
- different output in processors
- different results for parallel vs serial runs for NAMD
- Difficulties is minimizing capped peptides
- Difficulties is minimizing capped peptides - solution
- Diffusion of Protein through the membrane
- Dihedral energy not getting generated ( is zero )
- Dihedral Parameterization
- Dihedral parameters for multiple minima
- Dihedral restraints do not work
- dihedrals multiplicity in xplor psf file
- dimer minimization
- dissociation in NAMD
- dissociation of water
- distance constraints with an upper bound
- Distance restraint
- distance restraint w/upper bound example
- distorsion in hydrogens added
- Dixitpd wants to Share Favorites with you
- DMPC Atoms moving too fast !
- DMPC psf.
- DNA and low pH
- DNA H-bonds
- DNA helix model
- DNA hydrogen bonds
- DNA protonation
- Do I need to use an xsc file to restart a simulation in NVT?
- Do we need to renumber atoms after solvate?
- Does pair interaction calculations uses PBC ?
- Does rmsd is the judge of system equilibrium in all conditions?
- Don't get mad, get Val1um!
- Double bond-pheyl group bonding parameters
- double precision numerical accuracy issue
- Downloading CHARMM Parameter and Topology Files
- DPMTA instead of PME without PBC possible?
- DPPC.Pdb
- DPPC.Pdb file needed
- Drift in performance
- drift in protein membrane simulation. membrane and protein one way, water the other way
- dual core processors
- dublicated residue numbers in PDB/PSF
- dummy atoms and FEP
- Dummy particles
- Dumy atoms in FEP
- during namd build / compile -ltcl8.4 linking error
- effects of box size
- electric field
- electric field and MISC
- electric field and MISC energy
- energy calculation in VMD
- energy drift in NVE
- Energy due to electric field
- Energy Minimization
- energy per residue
- Energy Plugin
- Energy shift during simulation
- enery evaluation inside Tcl-Forces?
- eq. info.
- equilibrating the system with constrained Protein
- equilibration
- equilibration at three different temperature
- equilibration of "big" membrane
- equilibration of protein
- Equilibration problem
- Equilibration with constant temperature and pressure
- Equilibriation Info
- error about tclForcesScript
- Error bad vdW format in Charmm parameter file
- error caused by atoms of lipid membrane
- error caused by lipid membrane
- Error compile charm++
- Error compiling NAMD with MPI
- error estimate in FEP calculation
- Error in equlibration
- error in loading "import hessian/charge from single point calculation" in paratool
- error in membrane producing
- error message
- error message in free energy pert.
- error messages in log file
- Error on renaming file
- error on running NAMD on a large cluster with prun
- Error on the constraints
- error related to tcl boundary forces
- error using Namdenergy
- Error: Compile charm-5.9 on Fedora core 6?
- error: DID NOT FIND NIMPHI AFTER ATOM LIST IN PSF
- ERROR: Number of pdb and psf atoms are not the same!
- Error: parameter multiplicity.plz reply.
- Errors during equilibration: segmentation fault and bad global exclusion count
- errors in energy minimization
- Expansion of DCD
- experimental phi-values as restraints
- explicit hydrogen bonds
- Extended System Conservation
- extended system or Basis Vector
- external force
- extra lines in PSF !!!
- extracting coordinates from dcd file
- extracting forces from dcd files
- extracting interaction energies
- extracting waters from DCD
- Extraction of force data
- Factorization in PMEGridSize
- fad topology and parameter file
- Faltal Error. reassignFreq fails
- Famous repl1ca w4tches r0lex Cartier Bvlgari
- FAO developers: vdW energies, forces and derivatives
- farnesyl&retinal
- Fast routines for distance evaluations using PBC.
- Fat node
- FATAL ERROR: Bad global exclusion count
- FATAL ERROR: Bad global improper count!
- FATAL ERROR: called "save_callback" with too many arguments when running replica exchange
- FATAL ERROR: DIDN'T FIND vdW PARAMETER FOR ATOM TYPE CAI
- FATAL ERROR: pairlist i_upper mismatch!
- FATAL ERROR: Tried to find atom type on node other than node 0
- FATAL ERROR: Unable to open extended system file.
- FATAL ERROR: UNKNOWN PARAMETER IN CHARMM PARAMETER FILE
- faulty kernel?
- FEP & different ligands
- FEP Energy very high: Mutual exclusion of atoms
- FEP error "atoms moving too fast"
- FEP implementation in NAMD
- FEP implementation in NAMD - ERRATUM
- FEP in vacuum
- FEP question
- Fep questions about FepEquilSteps
- FEP, IONS, DUMMY atoms, LARGE numbers
- FFTW problem
- files for air
- finding free energy at a time step using abf
- Finding size of water box
- first aid
- firstLdbStep and ldbPeriod
- fix atoms in minimisation
- fixed atoms appearing on the other side of simulation box
- FIXED atoms not included as described in the documentation
- fixed system just in Z direction
- FixedAtomForces and ExcludeFromPressure
- fixing internal coordinates
- flexiblecell and constant ratio
- fluorescent probes
- Flushing output: MPI version of NAMD on AMD64
- Flying ions
- follow up question about heating the system
- For slowly heating, temperature reassignment or Temperature coupling
- for the isntall and run NAMD soft on 8 core (dual quad-core Xeons) system
- force calculation
- force calculation during to conformational change
- force constant for zer-velocity SMD
- force constant from gaussian to namd
- force constant matrix
- force dcd files??
- Force field for coarse grained simulations (and other questions)
- force field for H2PO4- and HPO4(-2) ions
- force field parameters for fullerenes
- force on SMD atom
- force over selection
- force-field parameters for glycoproteins
- force-field parameters for TOAC
- forces calculation
- forces on atom
- forming disulfide after equilibrating system
- Fortran and tclForces
- forward and backward pulling
- Free Cluster-Building Workshops - 16-17 Mar 2006, 20-21 Apr 2006
- free energy calculate
- Free energy Calculations
- Free energy from MD Simulation
- Free Energy of Conformation Change
- Free Energy of Conformation Change Units
- Free energy perturbation of a double mutant
- Free energy with amber topology
- free energy,energy,entropy calculation for pushing ATP to active site of kinase!
- Free Energy/ ERROR
- Free Linux Cluster-Building Workshop - 30 Nov 2006 - 01 Dec 2006
- Freezing point
- FullSamples variable in ABF
- Fwd: Determining Transition State from an Unfolding Simulation
- Fwd: extracting waters from DCD
- Fwd: Fwd: Water Box size
- Fwd: GRADIENT TOLERANCE: nan
- Fwd: Laptop for Molecular Dynamics - Summary
- Fwd: namd2 installation..
- Fwd: Water Box size
- FYEO
- g(r)
- g(r) plugin
- Gas phase minimization
- General question about psfgen atoms.
- general question on protein-membrane simulations
- general question on protein-membrane simulations -complete message!
- generalized born routine
- Generalized solvent boundary potential or similar tricks for huge systems in NAMD??
- Generating a gromacs topology file for analyzing NAMD trajectories
- Generating lipid bilayer model
- generation of non-standart charmm topology
- getbond (Tcl forces) / PBC
- getting #.IND #QNAN after phase 8
- Getting density of water..
- Gigabit ethernet switch for cluster
- Globus-WS Submission of a NAMD Job ..
- GPU acceleration press
- gradient for minimization
- gradually pressure change (increase/decrease)
- guesscoord fails, hydrogen adding problem, output pdb is all zeros
- H-bond energy
- Happy Viagra
- Harmonic Constraint: 2 types
- Harmonic dihedral restraints
- harmonic distance restraint
- has anyone patched NAG to ASN?
- HD speed ??
- heat capacity: NPT vs. NVT
- heat diffusion
- heat diffusion calculation
- heat flux when using langevin dynamics
- heating system
- Heating Up a system.
- heating with restraints
- help
- Help !!! ERROR: Atoms mooving too fast
- Help Needed>Compiling source namd mpi enabled for a linux cluster
- help on compiling error
- help on error message during compiling
- Help on mutation
- help on NAMD code
- help with adding a new force filed into NAMD
- Help with TCl script
- help! How to build charm++ on core 2 computer processor
- help!!
- help!!!
- help-minimization and equilibration of Ubiquitin in a water box
- Help. Parameters for PSGL needed
- help: how to scale the velocities by a factor for a subset of the system?
- help:autopsf changed the structure!
- Heme - Cysteine link
- Hexagonal boundary conditions
- hexagonal box
- hexagonal crystal
- Hi
- hi...
- High background load warning message
- High VDW energies during minimization and dynamics
- high vdw energy
- HIS to HSD, HSE, and HSP
- histidine protonation
- History file of an ABF smiulation
- Hoe to create psf file of C-terminous of protein?
- how add bond in psf file?
- How can I do protein complex's simulation?
- How can I get parameters of unknown residues
- How can I use TIP4-P water model with NAMD?
- How could I find which part of the protein became more flexible
- How could I fixed the system just in Z-coordinate?
- how gradually change (increase/decrease) pressure ?
- How is the maximum velocity limit set?
- how long is enough to heat up and equilibrate
- how long should the simulation be run
- How to "twist" a molecule?
- How to "twist" a molecule? (resubmit)
- How to access energies after MD step with Tcl ?
- how to add charged particles manually.
- how to apply different damping coefficients simultaneously to different atoms in the same system.
- How to avoid => ERROR: Step 100920 cell rescaling factor limited.
- How to build charm++ on core2 processor
- How to build the psf file and the parameter file of a ligand
- how to caculate the hydrogen bonds occupancy?
- How to calculate the C alpha RMSD from NAMD trajectory
- How to compile NAMD2.6 on core2 operons, x86_64-redhat-linux,which is the proper choice in Arch.
- how to constrain a dihedral angle?
- how to constrain a dihedralqangle=3F?=
- How to construct .prm file of phospho-THR?
- How to contract the PBC cell
- how to convert dcd files from namd to charmm
- How to create psf for carbohydrate
- How to create repulsive particle ?
- How to deal with a long path in ABF simulation?
- How to deal with this sugar residues though psfgen?
- How to define a spatial grid for a temperature landscape/contour
- how to do free energy perturbation calculation in NAMD?
- How to evaluate the area per lipid and thickness of a lipid bilayer?
- How to freeze some atoms
- How to get around with "atoms moving too fast"
- How to get different kinds of harmonic constraints in one script?
- how to get the velocities from the dcd file
- How to implement an additional interaction potential?
- How to include more parameterfiles in NAMD
- How to include parameters from stream files in calculations
- how to install rmsdtt in Windows...
- how to kill namd job in TCL FORCES Script?
- how to kill namd2 child process after power cut
- How to link two proteins
- How to load velocities during simulations.
- How to make a disulphide bond
- How to make a virtual bond?
- How to make alkaline ph pgn file
- how to make dual-hybrid topology?
- How to measure of radius of a molecules?
- How to model HCN gas molecule by NAMD?
- How to patch residues in different chains
- how to perform MD with two proteins
- how to plugin catDCD into VMD of windows version
- how to plugin catDCD intoqVMD=20of=20windows=20version?=
- how to remove translational and rotational motion from dcd file
- How to restart a simulation
- how to restart FEP
- how to restart/continue NAMD run
- how to simulate sugars
- How to turn off electrostatic interactions (PME).
- How to unsubscribe ?
- how to use measure hbonds to calculate occupancy of all hbonds in simulation?
- How to use NPT ensemble to fix water density
- how to use reaction field in NAMD
- How to use the transformation matrix in VMD to obtain the tetramer
- How to write a new dcd.file by using Tcl
- howcan I use amber forcefield in NAMD?
- Howto lengthen a collagen strand (which tool to use)
- hybrid qm/mm
- Hydrogen Atoms and Water Molecules
- Hydrogens collapsing
- Hydroxyproline topology
- Hymen destroyer
- Hymen penetrator
- I want to know how to make pdb file with 2d structrure file.
- I'm sorry ... please ignore the junk !!
- If I run NAMD on small computer, which processor is the best for NAMD under Linux?
- IMD-host name-port number-connection problem.
- Implicit solvent simulation
- imprecision in table energy
- improper torsion
- Improve your sexual life and save up to 80%
- Incorrect Atom Count
- InfiniPath and NAMD
- Infinite Armchair Single Wall Carbon Nanotubes and Periodic Boundary Conditions (PBC)
- infinite layer
- infinite nanotubes with PBC in NAMD?
- Info: Adjusted background load on 11 nodes.
- Initial and final state fix MD
- input file for PO3
- Installation Problem
- Installing NAMD
- Installing NAMD 2.6 on SMP machine... charm++ install errors
- Intel Woodcrest version?
- Interrupted system call
- Invalid cpus 2 in nodelist ignored
- Ion Channel Jarzynski
- Ion-protein and protein-protein interactions
- ionize (big, big, big system!)
- Is clock skew a problem for charm++
- Is clock skew a problem for charm++)
- Is it equilibrated?
- Is it possible to compile NAMD win64 with MPI (windows MPI)
- is possible to remove the waterbox before running VMD
- Is the GBSA model in NAMD ?
- is there any maximum limt of atom numbers in VMD or NAMD?
- Is there solution to numerical inaccuracy
- Is very slow heating "bad"?
- Issue with rhombic dodecahedron / CHARMM compatibility
- It doesn't work with using amber files.
- Itanium_and_CMAP
- job stall w/ incresed cpu usage
- Jump in Electrostatic Energy between two values
- Just can't seem to compile charm++
- Kinetic Energy frm MDEnergy (energy evaluation tool)
- langevinHydrogen off?
- Laptop for Molecular Dynamics
- Laptop for Molecular Dynamics - Summary
- Large Benchmarks
- Large energy fluctuation
- Latency vs Bandwidth over Infiniband
- LDB problem on Dual Atlon64 X2
- length of an ABF simulation
- LES
- les + conformational free energy
- LES / cLES
- LES : size
- LES and minimalization
- LES with PME and neutralizing charges
- libstdc++.so.5
- Ligand Bound.
- ligand parameterization
- ligand parameters... I know the next step
- ligands parameters
- Light dummy atoms (source code question)
- line too long in pdb file restart.coor
- LINE=*CMAP*
- Linking with -memory paranoid
- linux cluster problems
- Linux HP Itanium Quadrics
- Lipid bilayer center go away from center of system.
- Lipid into NAMD
- Lipids into NAMD
- lj parameters for gold for NAMD
- load balance strategy query
- load balancer, athlon 64 dual core
- load balancing question
- loadforces problem
- loadtotalforces error
- lock / unlock threads
- log File - pressure not read
- long range electrostatics for alchemical transformation
- looking for paramter
- Maestro Penis
- make the helix longer
- many short runs or one long run?
- Margin Error
- margin error message
- margin value
- mass of atoms changable?
- math formula for spherical boundary conditions.
- MD analysis
- MD in a loop with different names for dcd files
- MD in steps
- MD of DNA
- MD problem
- MD Run frozen
- MD runs at different clusters
- mDyne/A to kcal/mol/A2
- Meaning of lines in "run" part of log file.
- mechanical force calculation
- Membrame Volume Increasing after restart
- membrane constraints on thickness
- Membrane Protein Simulation Problems
- membrane simulation: pressure control parameters
- Membrnae (POPE)/protein simuliation.
- Memory requirements for clusters
- Minimization
- Minimization algorithms
- minimization error - high IMPRP energy
- minimization of a cyclic peptide with NAMD
- minimization temperature and constraints
- Minimization using Fixed Atoms
- minimization-problem
- minimize in FEP....
- Minimizer
- Minimizing and Equilibrating
- minimizing bad system: bad global excl. count
- minimum energy frame
- minLineGoal comannd
- mismatch of topology with parameter file
- missing atoms in pdb file.
- missing info from NAMD output
- MM works MD does not in Fixed system
- MMPBSA...
- MMTools/PCA
- Modeling HCN.
- modeling zinc binding site
- modified patch to PROline
- Molecular Volume
- Molecule drifts and high average RMSD per residue
- molecule leaves water box during md
- Morse potential?
- MPI compile of NAMD runs on dual core machines but not quad core machines
- Multi Harmonic constrains
- Multimeric protein
- Multiple constraint file
- Multiple residues at same position
- Multiple tclForcesScript
- multiple tcouples?
- multiple time stepping in namd: Query
- multiple timestep and dcdfreq
- multiple topology files
- Multiplicity of Parameters
- my simulation dont be minimized when I fixed the channel
- n terminal patch on proline
- N-methylacetamide
- NAD splits up into 3 pieces
- NAD topology and parameter file
- NAMD + nice
- namd + opteron/xeon
- NAMD - Pronunciation?
- namd 2.6 installation on i686 problems
- NAMD 2.6 installation problem
- NAMD 2.6 released
- namd 2.62b FATAL ERROR: Memory allocation failed on processor 0 or higher
- NAMD 2.6b1 released
- NAMD 2.6b2 on IBM POWER5 with AIX 5.3 Operating System
- namd and amber force field
- NAMD at NCSA
- NAMD Carbohydrate Simulations
- NAMD cg configuration file
- NAMD compile in Mac OSX and IBM XL C/C++
- NAMD configuration files for NVT ensemble
- NAMD constraint force and energy
- namd crash: Signal: segmentation violation
- NAMD crashes on winx64 during parallel run.
- NAMD fails on Altix
- NAMD fails with LAM (can't run example)
- NAMD for inorganics??
- NAMD hangs at "OPENING EXTENDED SYSTEM TRAJECTORY FILE" / PME error
- NAMD hangs in parallel on OSX
- NAMD in Solaris X86
- NAMD install problem.
- namd installation
- NAMD Installation - SUSE Linux 9.1 on IBM X Series 335
- NAMD installation on Cray XD1 (AMD opteron 64-bit)
- NAMD installation on Xeon64 cluster
- NAMD Installation Problem
- NAMD Integration algorithm
- NAMD is unstable on myrinet connecting cpus
- NAMD ligand
- NAMD Linux LAM/MPI 7.1 execution error
- Namd list administration
- NAMD memory leaks on AMD Opterons using MPICH-MX
- NAMD memory problems on ASC's SGI Altix machine
- NAMD message
- NAMD not starting calculations...
- NAMD octahedron
- NAMD on Abe
- NAMD on CELL BE
- NAMD on dual core, dual processor machine?
- NAMD on Dual processor computer
- NAMD on dual quad-core Xeon's with Infiniband backbone
- NAMD on Infiniband - problems and successes
- NAMD on Linux IBM PowerPC JS20 Cluster
- NAMD on Power5
- NAMD on RedHat Linux
- NAMD on TeraGrid
- NAMD on TeraGrid: OpenMP?
- NAMD OSX Xgrid
- NAMD pairInteraction - huge VDW and TOTAL3
- NAMD Parameter File Creation
- NAMD plot plugin
- NAMD question
- NAMD results depend on # of processors!!??
- NAMD run
- namd seg fault on Intel cluster
- NAMD support for MNDO semi-empirical model
- NAMD timestep and numsteps
- NAMD to Amber
- NAMD to CHARMM unit cell information in DCD
- Namd window network problem
- NAMD with Myrinet MX on MacOS X
- NAMD-2.6 Insatallation help
- namd-l : Topology info - RESidue information for carbon nanotube
- namd-l-outgoing2@halifax.ks.uiuc.edu
- NAMD-L: question about harmonic constraints
- NAMD-L: question about SMDk, the force constant for SMD
- NAMD-L:density of water molecules in a water sphere
- NAMD-lite - Heun's method implementation
- namd.conf with OPLS options
- namd/charm infiniband build
- NAMD/Infinipath installations
- namd2 installation..
- namd2 on IBM P5 hangs
- namd2 run error
- NAMD2.6 requirments on p690
- namd2.6b1 has bad scaling
- NAMD2.6b1 on MAC cluster problems
- NAMD2.6b1 on MACOSX
- NAMD2.6b2: Segmentation fault
- namd: adding water molecules
- NAMD: compile problem
- namd: DSPC and DAPC for a phospholipid bilayer
- NAMD: Exiting Prematurely
- namd: problem
- NAMD: run problem
- namddat
- namddat syntax error
- NAMDEnergy
- namdenergy plugin
- namdenergy strange behaviour !!!
- namdstats gives nan's in tutorial output
- Nanopore simulation
- NBFix and NAMD
- NBFix not working with charmm par file
- NCSA Abe versus TACC Lonestar
- NDON! and NACC! in Parameter Files
- need pair interaction energies, not forces
- negative force
- negatively charged proline as substrate
- Net charge of the system is not zero
- net translation in long simulations
- New ABF order parameters
- New alchemical FEP tutorial
- new spam filtering
- NNB in PSF and alchemify
- No effect of periodic boundary conditions?
- no effect on velocity scaling
- no Na or CLA paramters in par_all22_prot.inp
- no parameter for CN8-ON6
- Nobody will know about your problems.
- non-cubic boxes for Periodic Boundary Conditions
- non-parallel NAMD compilation
- nonbonded interactions
- nonbonded interpolation
- Normal mode analysis
- Nose-Hoover langevin piston pressure control and target surface tension
- NPT ensemble with Periodic boundary condition
- NPT_NPgammaT_or_NPAT_for_membrane_with_CHARMM_forcefield
- Number of atoms to high for mdenergy
- nve ensemble
- NVE ensemble configuration file
- NVT nose-hoover hamiltonian in SMD?
- One question about running NAMD
- one residue rmsd
- One Year written repl1ca w4tches warranty
- only minimization
- OPLS dihedrals
- OPLS force field for carbon tetrachloride ( ccl4 ) ?
- OPLS force field in namd
- OPLS Lipid topology/potenital for NAMD
- OPLS-AA/L
- Orgasm power
- Orgasmotron
- other crystal types in NAMD ?
- output on Linux-amd64-MPI
- outputPressure
- Overlaoded processors when running NAMD on NCSA Altix
- OXT in pdb file
- pair interaction
- pair interaction analysis of multiple trajectories with different timestep
- pair interaction cutoff
- Pairinteractions
- pairinteractionSelf
- Pairlist warnings
- parallel NAMD output problem
- Parallel performance on Intel Woodcrest
- Parallelization method
- Parameter
- parameter and topology file for ethanol
- parameter and topology for cyclodextrin!
- parameter file for DAD
- Parameter file for Gold ?
- parameter file name
- parameter files
- Parameter or patch for thioester
- Parameter resetting in NAMD
- parameterizing a beta aminocyclohexanecarboxylic acid
- Parameterizing ligands with protein
- parameterizing novel molecule
- parameters for camphor
- parameters for GABA (gamma-amino butyric acid)
- Parameters for NH3, NH4+, and CO2
- paratool for MG
- part of a protein
- Partial charges on amino acids
- particle access in tclBC
- patch in psfgen...
- Patch needed for tuple is missing Error with POPC bilayer
- Patches & psfgen
- PBC related query
- pbc_box
- PBS & local (scratch) space
- pdb file
- PDB residue renumbering
- Penis Launcher
- peptide conformation search examples
- peptides confined in a water sphere
- Performance Problems on Linux Cluster / Bad Scaling
- Periodic boundary conditionds-Surface Energy
- Periodic boundary conditions
- periodic boundry conditions
- Periodic Cell error on CO2 MD
- Periodic cell has become too small
- Periodic cell has become too small for original patch grid!
- periodic cell too small
- Periodic Run Crash
- Periodic velcoity pulls
- pH in NAMD
- phi and psi dihedral restraints
- please help-large energy change during FEP calculation
- plz help!!
- PME for a hexagonal system
- PME grid error during minimization
- PME GridSize
- PME on a negatively charged system
- PME on a negatively charged system.
- PME pair interaction analysis
- PME processors
- PMEGridSize
- PMF
- pmf calculation
- PMF error
- PMF of SMD using CHARMM generated trajectories
- pmf segname for amber ff. MAIN?
- PMF, defining end point
- PO3 psf
- Poisson Boltzmann with NAMD
- Polarizable force fields
- polyethylene topology
- POPC
- POPC bilayer- System size
- popc pressure profile
- POPE/protein simuliation.
- positive VDW??
- Possible bug on NAMD 2.6B1?
- possible error warning
- Potential function (force field) in NAMD
- Potentials of mean force using ABF
- Power penis
- Premature stop
- Prescr1ption med1cations... without a prescr1ption!
- Pressure -ve
- pressure calculation in applied field
- Pressure calculation method
- Pressure control
- Pressure Discrepancy
- Pressure Driven flow of Water
- Pressure fluctuations
- Pressure problem when using restart file
- pressure vs density tip3p
- printing and global variables within TclBC script
- prob. with constraints
- Problem about cellBasisVector
- Problem about momentum correction
- problem about pairlistdistance...
- Problem about the energy change of refold of SMD protein
- problem building Namd frm source...
- Problem compiling NAMD on BlueGene
- Problem en equilibration Protein into a bilayer membrane POPC
- Problem equilibrating with low pressure
- Problem for to use/compile NAMD with mpiexec
- Problem heating the system
- problem in minimization while running
- problem in running equilibration
- Problem in Running namd2
- Problem on NAMD simulation energy output
- problem reading topolgy files
- Problem setting distance restraints
- Problem to run IMD simulation
- problem w/ free energy perturbation
- problem with *.pdb and *.psf
- problem with ABF "can't read forces(80)"
- Problem with Alchemical FEP
- Problem with biotin autopsf
- Problem with C++ libraries
- Problem with center of mass movement in simulation
- problem with dihedral restraint
- problem with Dihedral Restraints
- Problem with equilibration and pressure
- Problem with NAMD and constraint failures
- problem with NAMD RNA run
- problem with namddat_unix: Plz help...
- Problem with NVE run: Help
- problem with periodic boundaries
- problem with reassigning temperature
- Problem with VMD 'animate' command
- Problem with water box
- problems compiling NAMD on SCALI architecture
- problems for runing NAMD on parallel computers
- Problems of mpi with namd 2.6
- problems of RATTLE with big systems
- problems reading large dcd file
- problems replicating a DOPC membrane
- problems running more than 9 Replicas in replica exchange simulations
- problems running Replica Exchange simulations using SSH to spawn the processes
- Problems with (Restrained) TMD in NAMD
- problems with .conf script
- Problems with energy conservation in NVE dynamics with 2fs timestep
- problems with mutation in psfgen
- Problems with Mutator1.1, mutations and FEP
- problems with paralellism
- Problems with using multiple Tclforces scripts sequentially
- Problems with version 2.6 for amd64
- production in NVE ensemble after equilibration in NPT ensemble
- Products that can improve you life!
- protein diffuses to boundary..
- Protein hydrogens causing "Atoms too fast" error
- Protein in/out of box
- protein is moving from center to one corner of water box.
- protein moves away from water box
- Protein partially denatures during pulling
- protein spinning and total enegy not constant in NVE
- protein unfolding -- Phi MD
- Protein, ligand, ion out of the water box.
- protein-DNA complex
- protein/lipid simulation
- protonation of some histidine residues
- Protonation state
- Protonation states
- PSF file
- psfgen and bond topology specification
- psfgen and charmm19: is there any inconsistency?
- psfGen error
- psfgen for pre-equilibrated membrane bilayer
- PSFGEN for protein containing GTP
- psfgen gets ATP chiral atoms wrong
- psfgen operation for the C terminal of HSE
- psfgen problem
- psfgen: last CTER does not work
- psfgen: merging of 2 dna chains
- ptraj
- Pulling of Center of Mass
- pure TIP5P water system with AMBER7 parameters
- Push ATP to active site of kinase!
- Q=D4=D7=C5=D4:__128+_proccessor_jobs_on_64bit_?= Widows hang upon completion of the simulation.
- Qmeasure=22?= command
- qsub on a linux cluster
- Queries on patches, GDP-topology
- query about thermostat..
- query about wrapped coordinates
- query about wrapped coordinates: Problem SOLVED
- Question about ABF
- question about ACE and NME patch
- Question about compiling NAMD
- question about equilibration step
- question about FEP calculation
- Question about free energy of conformation change
- Question about memory usage
- question about protein leaving water box
- Question about REMD
- question about RMSD defined in NAMD
- question about the influence of water box size in FEP
- question about the parameter "exclude"
- question about total charge change in FEP calculation
- Question about Van der Waals radii
- Question for 2D periodic boundary condition
- question on 1-4scaling factor
- question on free energy pert.
- question on heating
- question on membrane crushing
- question on membrane protein simulation
- question on membrane simulation
- question on mutate command in NAMD
- question on pairinteraction
- question on phosphotyrosine parameters from charmm
- question on pulling direction
- Question on simulation energy output
- Question on SMD simulation in spheric water .
- Question on the bond energy of NAMD tutorial
- question on the charged system
- question on the format of adding Lennard-Jones parameters
- Question regarding NAMD nonbonded routines
- question regarding nearest-image resolution in NAMD
- Question regarding SETTLE (RigidWater)
- question regarding the use of reaction coordinate "distance-com" in ABF method
- question switching function
- questions about the use of HIS residue
- questions regarding output data of an ABF simulation
- questions regrading ABF
- radial distribution function
- Rattle Algorithm
- RATTLE algorithm error
- Rattle Error
- RATTLE error and GROMACS parameters
- Rattle Error During Equilibration of Lipid Bilayer Membrane
- RATTLE errors in equilibration
- RATTLE failure
- RDF.tcl
- RDF.tcl question
- Re velocity error
- Re. Namd window network problem
- read dcd binary trajectory
- reading a binary restart file
- Reason: FATAL ERROR: Simulation config file is not accessible.
- Reassign temperature for selected atoms?
- Reassigning Velocities
- recalculating energies
- Recentering the box on target molecule and wraping
- Recommended solvation box size
- recompiling NAMD 2.6 from sources on CentOS-3 x86_64: Charm++ failing test
- reconstructing PMF
- redirecting stdout to a file
- reflective barrier
- Regarding box-size
- Regarding Trajectory analysis
- REMD
- REMD using PBS qeue
- Remove water to close to the protein?
- removing bonds in psf
- removing waters from big dcd files
- Repeating again: Periodic velocity pulls
- Replica Exchange
- Replica Exchange (Parallel)
- Replica exchange error message
- Replica exchange MD
- Replica Exchange MD using Amber parameters
- Replica Exchange NAMD
- replica exchange trajectories
- Replica Exhange error: POSIX EINTR {interrupted system call}
- Replica-Exchange MD
- replicating a DOPC membrane
- replies
- Report
- reproduciblity between software
- Reproducing free energy profile for acetate-guanidinium association
- residue name and segment name
- Residue name for Dimethyl sulfoxide
- residue name LIP ... !
- residue_rmsd.tcl question
- restart a NAMD simulation after coordinate transformation in VMD
- restart a NAMD simulation after coordinate transformation in VMD (solution)
- restart a simulation
- restart NAMD job
- Restart Simulation
- restart the simulation
- restarting an AMBER simulation (truncated octahedron PBC) in NAMD fails
- Restarting calculation missmatches
- restarting the simulation
- Restarting velocities
- restraining backbone atoms
- restraining parts of a molecule
- restraining the protein not to move during equilibration
- Restraints and System COM Drift
- returning the host list where NAMD runs from an LSF batch system
- Re£º difference in total energy values
- re£º force over selection
- Re£º question on 1-4scaling factor
- Rigid body minimization
- Rigid bonds
- Rigid bonds for United Atom Methylene Chloride CH2Cl2
- rigid protein
- rmsd calculation for RNA
- RMSD increases after restarts, decreases at the end of run
- rmsd is not stabilizing even after 0.6 ns
- rmsd_fullthrotle script problem
- RNA to DNA
- run frozen
- Run NAMD in loops
- running 2 jobs simutaneously?
- Running Error: The periodicity of dihedral #2 is zero
- running NAMD on beowulf cluster
- Running NAMD on Cluster machine with Myrinet network with MPI and PBS
- Running NAMD on debug mode
- Running NVT simulations
- Running thermal unfolding with nose hoover langevin piston
- running_NAMD_on_ALPHA_workstation
- same random numbers??
- SAMs using NAMD
- Saving coordinates of each frame into one separate .pdb file from a 100-frame .dcd file.
- saving the coordinates for huge trajectory file
- Saving the coordinates of DCD file in pdb format
- Say "NO" to erectile dysfunction!
- Scalability problem with NAMD2.6 on Intel Xeon EM64T processors
- Scale
- scaling issues in distributed environment
- scaling NAMD2.6B1 on IBM P5
- Scaling the Tiny benchmark
- scripting in namd
- Scripting: Handle for energy terms in the PSF file?
- segmentation fault: Please Help
- Segmentation violation from APOA1 simulation on AMD64
- Segmentation violation when running without an internet connection
- seperate files-par, top and pdb files for solvents, needed?
- serine phosphorylation modeling
- setenv: command not found
- setting solvent density during solvation
- Sexual power
- SGE and NAMD
- SHAKE: Constrain EVERY bond length and bond angle
- sialic acid
- SIDECHAIN _RMSD
- SIDECHAIN _RMSD_Thank_you
- simple query..
- Simple TCL (Forces) question - defining bond vector
- simulated annealing
- Simulated annealing out of mainstream
- simulated annealing with explicit water
- Simulating air with NAMD
- Simulating the orientation of detergent and lipid molecules around a membrane protein, bacteriorhodopsin
- simulation and equilibration
- simulation crashing with nan
- Simulation explodes as soon as minimization starts "GRADIENT TOLERANCE: nan"
- Simulation failed during the stage of heat
- Simulation Hangs during minimization
- simulation in nve ensemble
- Simulation in vaccum
- Simulation in water sphere meet with a FATAL ERROR about Bad global exclusion count
- Simulation of a 1000 water molecules
- Simulation of Eukaryotic membrane protein
- simulation of fullerenes
- Simulation of large bilayer crashes with "ERROR: Stray PME grid charges detected"
- simulation of membrane-protein systems
- Simulation on AMD64 Dual Core - threads lose connection
- simulation problems
- Simulation with denaturants?
- simulation_of_big_membrane
- simulations of periodic lattice
- Simulations with large number of constraints crash at startup phase 1 on Indiana's Bigred
- Single point energy?
- size of water box
- slow NAMD simulations on a AMD athlon64 in SUSE linux
- small query...
- SMD
- SMD and CPT?
- SMD and CPT? (fwd)
- SMD and restart
- SMD atoms are not moving in accordance with steering parameters!
- SMD behavior
- SMD Constant Velocity: Force
- smd dimer dissociation
- SMD Energy
- SMD ensemble?
- SMD From Force to Free Energy
- SMD of proteins in water box without PBC
- SMD of small molecule dimer
- SMD of small molecule dimer]
- SMD of TFIIB
- SMD of TFIIB!
- SMD on center of mass
- SMD on center of mass]
- SMD question
- SMD temperature scaling
- Socket closed before recv.
- solvating a protein
- solvating long protein
- Solvating protein with ions
- Some basic questions about NAMD
- Some problem on pair force calculation
- something about simulation of small molecules in NAMD
- sound velocity of water
- SPC/E water model
- Specific Heat Calculation with VMD
- Specific Heat Calculation with VMD]
- Specified Electric Field
- spherical boundary conditions
- Spherical harmonic restraint
- sphericalBCk1
- Spike during minimization of protein with water
- splitting up long run leads to very different DNA conformation in E field
- Starting out with NAMD/VMD
- starting simulation in charmm, continuing in NAMD ?
- Stationary temperature gradient - defining 2 langevinFiles?
- steered md with a constant velocity pulling
- Steered MD with NAMD?
- still on tcl boundary forces
- Still problems with heating
- Storage of large files
- Storing atom coordinates at each time step
- Straining yourself when you are with a woman?
- strange memory behavior
- Strange termination-possible load ballancing issues
- Stray PME grid charges detected
- Stretching Deca-Alanine
- STRIDE Algorithm
- sugar topology files
- Sulphate Ion Parameters
- Sulphate Ion Parameters (fwd)
- Superctitiacal CO2
- support TIP5? doubt on high temperature MD
- surface tension
- Switch ON your penis!
- Switching Function
- Switching PSF files during a run.
- System after pressure change - confirmation needed
- system calls inside namd script
- System charge
- system density
- SYSTEM ENERGY MINIMIZATION
- System of POPC bilayer
- system rotates after equilibration
- tabulated potentials?
- target molecular moves away from water box
- Taurine parameters
- Tcl Boundary Forces
- Tcl callback, run, revert, measure
- TCL energy variables
- TCL forces and boundary conditions
- TCL Forces and Help on Script
- tcl forces help
- Tcl in NAMD (math::interpolate)
- Tcl parsing of NAMD config file does not work.
- tcl script for applying constraints
- TCL script for umbrella sampling
- Tcl Scripting
- Tcl scripting within NAMD configuration file
- Tcl, minimization and MD (Warning: I am a lazy ignorant)
- Tcl-forces query
- Tcl: callback, run, revert, measure
- TCL: force not a vector
- Tcl_BC: [nexatom] twice in script
- Tcl_Forces / 'loadcoords' loads NOT wrapped coordinates ?
- Tcl_Forces = pressure shifts while Langevin Piston is ON
- tclbc example scripts
- tclforces: force not a vector
- tclForces: relation between force and velocity
- tcouple vs langevin
- temp autocorrelation
- temperature and pressure control
- TEMPERATURE and TEMPAVG : nan
- Temperature Control
- temperature control for small molecule simulations in vacuum
- Temperature Control: Rescaling and Reassignment
- Temperature Coupling
- Temperature dependent unfolding..
- Temperature problem
- temperature reassignment
- TeraGrid Efficiency
- the "firsttimestep" conundrum
- The algorithm of nose hoover langevin pressure control
- The best medications for the best price
- The charged states of histidines in green fluorescent protein.
- The experimental data of POPE?
- The NAMD job do not go forward
- the patch between segments for multiple chains molecule.
- the patching problem in psfgen
- The problem of "SMD and smd.tcl"
- the relationship between system size and cpu numbers
- the size of membrane?
- Thermodynamic Integration (free energy of conformation change)
- Third node stops the simulation
- third time..can someone help!!
- Time of MD
- Timestep
- Timestep -- Can I use 2 fs timestep for 50 nanoseconds simulation?
- timestep in namd
- timestep in TMD
- Timestep.
- TIP3P or TIPS3P
- tip4p - namd follwup
- TIP4P examples
- TIP4P in NAMD?
- TIP4P water
- Tired of your poor health?
- TMD
- TMD and RMSD constrained dynamcs
- TMD and TclForces
- TMD constrained energy
- TMD in NAMD: cannot reach target
- TMD: different behaviour between serial and mpi versions
- TMPyP4 force field parameters
- To buy or not to buy?
- to heat up the system
- too large an area/lipid in POPE bilayers using membrane plugin
- Tools to "open" domains
- top par for NAG, BMA ?
- top_all27_prot_na.inp and par_all27_prot_na.inp
- topology & parameters for urea
- topology and parameter file for non aromatic nitrogen in ring system.
- topology file
- Topology file for Building Gramicidin A (tutorial)
- topology file with CT carbon
- topology files
- Topology info - RESidue information for carbon nanotube
- topology of carbon dioxide compatible with Charmm
- topology problem!
- Torque aplication with SMD
- TOTAL energy increase
- Total external work calculation in SMD-PMF calculation
- total force on atom
- total mol calculation
- TOTAL, TOTAL2 and TOTAL3
- Tpr
- tracing not available with CMK_OPTIMIZE
- Trajectory analysis
- trajectory extension
- Transition path sampling
- Transition state
- Translation to NAMD psf file.
- transmembrane electrical potential gradient in NAMD
- Treatment of a Neutral N-terminus
- TRIO
- Trouble with Charmm/PDB?
- Troubles with Free Energy of Conformation Change
- Trying to profile namd to look for memory leaks
- turn off intermolecular interaction
- Turning off forces in VMD
- Turning off tcl forces
- tutorial address
- two chain in pdb file
- Two NICs on each node?
- two references
- two references- I got them, thank you!
- Type of force values in the tclForces script.
- UAB BlueGene
- Umbrella Sampling for NAMD
- unable to open charmm parameter file in Window
- UNABLE TO OPEN XPLOR PARAMETER FILE alanin.params
- UNC Paths in the configuration parameters
- uncharged ends
- unequal PMEGridSizes
- Unfolding protocol..
- Unfolding simulations
- Unit cell angles information
- unit cell information from dcd file
- Unit cell information in binary output files
- Unit of harmonic restraint force constant
- Unit of Velocity in the Velocity files
- United Atoms in NAMD
- units of OutputMomenta
- Unnatural Bond lengths
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- unusual, periodic crash in Linux FC3/GM/MPI/CHARM/NAMD
- Update on NAMD on BlueGene/TCL
- updating TCL version for NAMD?
- Urea parameter
- urestraint for minimizations and MD (no PMF)
- Urey-Bradley term and VDW energy
- Use extendedSystem or cellBasisVector?
- UseConstantRatio between "run"
- useFlexibleCell
- useGroupPressure
- user defined L-J parameters
- User defined potentials of Lennard-Jones type possible?
- user defined restraint in ABF
- user defined restraints?
- uses of patches for changing the protonation states of residues
- Using CHARMM27
- Using CHARMM27]
- Using LES with AMBER parm files
- Using NAMD DCD in CHARMM
- Using NBFIX
- Using PsfGen
- using restart file or .coor/.vel file
- Using/converting old extended top and par files?
- value of B column is zero
- Vanishing bonds in small molecule during psf generation.
- variable cellOrigin
- Varying Force Simulations
- VDW energy in CHARMM force field
- vdw parameter
- vdW parameter for atom type CN7 in ATP
- vdW parameters
- Vega ZZ Script for calculating area/lipid.
- Velocities of different Atoms
- velocity error
- velocity error, still
- Velocity unit ofvelocity in NAMD the binary files
- Velocity Units
- Very peculiar problem while using bigdcd. Help !
- viarecv.c rhandle->len' failed. on infiniband
- Vibrational mode analysis
- Vlad has Tagged you! :)
- VMD Command
- vmd-l:
- vmd-l: 64 bit NAMD on AIX and CatDCD
- vmd-l: a display problem
- vmd-l: Aligning structures
- vmd-l: Angles and dihedral generation
- vmd-l: boubt about consistency of measures
- vmd-l: breaking the DCD file
- vmd-l: CMAP problem
- vmd-l: CoordinateTransformation
- vmd-l: DCD for windows
- vmd-l: DNA and low pH
- vmd-l: dummy atoms and FEP
- vmd-l: energy calculation in VMD
- vmd-l: error using Namdenergy
- vmd-l: Fast routines for distance evaluations using PBC.
- vmd-l: force over selection
- vmd-l: Generating PSF for 1JNO.pdb chain A
- vmd-l: How to calculate the C alpha RMSD from NAMD trajectory
- vmd-l: imposing period boundary conditions in a simulation with a crystal
- vmd-l: ionize (big, big, big system!)
- vmd-l: is possible to remove the waterbox before running VMD
- vmd-l: merging two pdb files
- vmd-l: Multiple residues at same position
- vmd-l: namdenergy plugin
- vmd-l: one residue rmsd
- vmd-l: parameter files
- vmd-l: problem in minimization while running
- vmd-l: Problem with VMD 'animate' command
- vmd-l: PSF files append!!
- vmd-l: psfgen: last CTER does not work
- vmd-l: Small molecules
- vmd-l: small query...
- vmd-l: too large an area/lipid in POPE bilayers using membrane plugin
- vmd-l: trace to newcartoon inconsistent display problem
- vmd-l: VMD Command
- vmd-l:namd-l; question about psfgen (param for CT1?)
- VMD/psfgen scripting: undefined variable
- VMD/psfgen scripting: undefined variable]
- volume exclusion
- Waiting for 0-th client to connect.
- wall clock vs secs/step metrics
- Want to be a hero in bed?
- Want to be on the top all night long?
- warning about pairlistdist:
- Warning: 1 processors are overloaded due to high background load
- Warning: overloaded due to high background load
- Warnings of psfgen
- water and air box by VMD
- water box deformation
- Water density is not 1.0g/cm3
- water HOH angle of 102 defrees
- water hole
- Water liquid-vapor interface
- water models: a basic question
- water molecules and silicon wall
- Water molecules inside protein?
- Water outside protein surface
- Water simulation with namd
- waterbox
- Wet miracle
- what does "patch" mean?
- what does "syntax error" mean in VMD? and does confinment to some residue will cause error?
- What happened when PBC is on but PME is off?
- What is an IC table in the .inp files
- What is an IC table in the .inp files]
- What's the highest temperature I can go?
- where is PSUL? Heme cystein link question?
- where to find the program DOWSER for setting water ?
- Where to put the "nodelist" file
- which binaries are best for SGI-Altix shared-memory?
- which charm
- which force field to choose
- Why does lipid move out of water box
- Why is SHAKE not being used in typical NAMD simulations ?
- Why is water density not 1.0g/cm3?
- Why minimization before Molecular Dynamics?
- why pressure is fluctuating so much
- why this error?
- Will reducing the cell basis vector in X and Y force my lipids to pack
- Win64 version
- working with non-protein files
- Worry about your erection?
- wrapping
- Writing to DCD file error - pelase help
- wrong simulation times or misleading time counting?
- wrong velocity in steered molecular dynamics
- Your dick is not only for pissing
- Your Pharm4cy 0rder #3728660
- zCoord-1atom
- zCoord-1atom and ** General remark: Subject lines **
- zero kinetic energy during minimization
- ZeroMomentum
- ZeroMomentum-Please help
- Zn parameters
- ´ð¸´: How to build the psf file and the parameter file of a ligand
Last message date: Thu Dec 27 2007 - 12:55:11 CST
Archived on: Wed Feb 29 2012 - 15:45:43 CST
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