NAMD-L: By Subject
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About this archive
Starting: Sat Jan 01 2005 - 14:57:24 CST
Ending: Fri Dec 29 2006 - 23:10:16 CST
- "Adaptive" force direction in SMD?
- "Hands-On" Workshop on Computational Biophysics
- "make" Linux-amd64-g++ error
- "measure" command
- "reinitvel" parameter in config file
- "Segmentation violation" on running namd2.6b1
- "wrapAll on" with a complex
- #QNAN: Please help!
- (no subject)
- 1 D Periodic Boundary
- 1-4 interactions scaling
- 2.6b1 source missing file
- 2D Ewald summation
- 4th Annual Workshop on Charm++ and its Applications 2005
- 64 bit NAMD on AIX and CatDCD
- =20?= qhow=20to=20constrain=20a=20dihedral=20angle=3F?=
- [Fwd: HD speed ??]
- [Fwd: increasing RMSD after 2 ns minimization-equilibration]
- [Fwd: SMD of titin domain]
- [Fwd: Specific Heat Calculation with VMD]
- a basic question
- a display problem
- a error during install charm-5.9
- a name quesiton
- A possibel wrong coding in Parameters::read_charmm_parameter_file(char *)
- A puzzling problem about adsorption energy in solution.
- A question about MD simulation of peptide.
- A question on minimization
- A question on psfgen
- A question on simulation with NPT ensemble
- A question regarding generate pdb and psf file
- A strange phenomenon in my dynamics system,any suggestion?
- a target molecule in a water box.
- abf
- ABF (fwd)
- ABF - zCoord for more than one monomer
- ABF for conformational analysis
- ABF on a single molecule
- ABF Simulation
- ABF with z-coord
- ABF.TCl file ???
- ABF: example works now; more questions.
- ABF: example works; more questions.
- About "get z" command in MD script language.
- About "mutate" command in psfgen package.
- about *.psf
- about abf
- About ADP
- About calculating RMSD with rmsd.tcl
- About charm++/namd on AMD64 cluster
- About CHARMM charge
- about counterions
- about diahedra entry in top_all22_sugar.inp
- About ions Representation in NAMD
- About Langevin Damping Coefficient.
- About Langevin Dynamics.
- About loadcoors -- is there a loadvelocity?
- About PDB file with fixed atom flags.
- About Potential Addition in NAMD
- About pressureProfile command for non-equilibrium system.
- about protonation of HIS in membrane protein
- About Restart
- About restart.vel.old file.
- about rigid bonds
- About RMSD calculation.
- about TCL boundary forces
- About the command "loadtotalforces"
- 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 potantial of IONS
- About the potential of NAMD
- About the Source code.
- About the unit of "efield"
- About timestep again.
- About timestep again. -- Fastest motion O-H streching period 10 fs.
- about topology generation
- ABSOLUTE IMPRECISION and RELATIVE IMPRECISION IN TABLE FORCE
- Accelerating groups of atoms
- Accessing beta / occupancy values from NAMD tcl
- ACE patch
- across the nodes, namd jobs don't get enough CPU!
- add ions
- add water on the top of the protein border
- added more bases to DNA using psfgen
- addforce
- Adding amino acids to an existing pdb structure
- adding extra ions to neutralize charge on protein
- Adding Misc. Potentials (e.g. spherical/repulsive restraints/constraints )
- Adjusting Density of waterbox used by solvate
- Alchemical Free Energy Perturbation
- Alchemical Free Energy Perturbation Simulation
- alchemical transformation
- alchemify FEP
- Aligning structures
- All or Nothing at All??
- Altix Performance Tuning
- Altix performances
- Amber and SHAKE algorimth
- AMBER ff system has too high velocities in NAMD
- Amber Parameter in NAMD
- AMD64 or PIV Prescott ...
- amidated C-terminus (NH2) with OPLS force field
- Ammasso interconnect performance, LDB question
- Analysis of NAMD output with CHARMM
- Angle 2, Where is the problem [IMPORTANT]
- Angle CO2 Problem
- ANGLE PARAMETERS (It works now)
- Angles and dihedral generation
- Another question about MD simulation of a domain.
- Another question on Diffusion
- any script to build membrane+protein+solvent?
- any SD minimization in NAMD?
- aquaporin question
- area of a hydrophobic patch
- area per lipid for a protein embedded membrane system
- Assign the ligand force field parameters
- assigning atom type for parameterization
- Asymmetric water molecule found???
- Atom distance & ptraj
- atom distances
- atom name based paremeters
- Atom Positions during simulation
- atom restraints
- atom specification in smd/tclforces for amber topology/parameter based systems
- atom type HZ4 not found
- Atomic partial charge
- atomlist command in matdcd
- Atoms moving too fast
- Atoms moving too fast error
- ATP in the Topology file
- ATP nucleotides using NAMD
- ATP PDB file
- autocorrelation analysis in timeseries
- autocorrelation function !
- AutoIMD
- autoimd on windows
- autoionize & namd2
- autoionize and psfgen, which one first?
- Autoionize error: spontaneously quits
- autoionize plugin..
- Autoionize: net charge NOT equal to zero
- Autopsf
- Avoiding Rotation and translation of protein
- bad exclusion count
- bad global exclusion count in LES
- Bad global exclusion count.
- Basic question about steered moledular dynamic(SMD) simulation
- Basic question.
- basic: combining two pdb files?
- Benzamidine parameters
- benzene in NAMD
- Berendsen pressure control problem
- Besides PSFGEN, (Thank you)
- Besides PSFGEN, are there any other good ways of generating .psf file
- beta-peptides ...
- Binary for MacOSX-i686
- binary restraint reference coordinates?
- binary.coor to ascII.coor
- Binding Energies for a Peptide-RNA System
- binding free energy , binding constant
- Bio-Image summer school in Paris this year
- Bizarre atom behavior
- Boiling temperature of water.
- bonding to image
- Box size
- box size changes under anisotropic pressure coupling
- Bromine
- Buffering problems while attempting to read log file
- Bug alert!!!
- BUG ALERT: Mother atom with hydrogenGroupSize of 0!
- bug in pressure calculation with E field?
- build script in charm++-5.9 does not find mpicc or mpicxx for mpi-linux version
- Building cluster
- Building for SunGrid
- Building molecule from topology file
- Building NAMD 2.6b1 on IBM Power5
- Building PDB files for DNA.
- bulid psf for structure already with hydrogens
- bulk density in RDF.tcl
- c-shell into NAMD configuration file
- CA CL CA angle?
- Ca trace only
- Ca++ topology¶m files
- calculate enthalpy of binding
- calculate potential energy from DCD file
- Calculating forces
- Calculating or Outputing Forces
- calculation (continue)
- calculation of non-bonded interactions
- Can any one help me with this parallel issue
- Can extending MIN solve the problem of "Constraint failure in RATTLE algorithm"
- Can I miminimize some atoms in system
- Can I use namd for carbon nanotubes?
- Can NAMD control pressure gradually increase?
- Can NAMD deal with solid-state system?
- Can someone PLEASE explain the "firsttimestep" parameter ?
- CAN'T FIND BOND PARAMETERS FOR BOND (error)
- CAN'T FIND BOND PARAMETERS FOR BOND FE - S
- Cannot open file 'pair.pdb'
- Cannot specify both an initial temperature and a velocity file
- capping using Amber FF
- caps
- Catdcd
- catdcd and dcdunitcell
- catdcd-generated files and CHARMM
- CCS ERROR during simulation
- Cell membranes with lipids different from POPC and POPE
- cellBasisVectors and xsc files
- cellOrigin
- center of mass motion: problems
- chage free energy
- Cham++ errors
- Chamrun/NAMD processes and PBS cluster
- change in Disulphide Patches
- Changes to dihedral angles
- changing default directory in VMD?
- changing file
- changing parameter files during simulation run
- changing velocity during simulation
- changuing dihedral angle slowly
- changuing dihedral angle slowly (complete message)
- charge on protein
- Charged Atoms in External Magnetic Field
- charges in topology
- charm++ 5.9 build fails, NAMD 2.6b1 make fails
- charm++ 5.9 megatest failure too
- charm++ compile problem on x86_64
- charm++ over MPI
- Charm++ problem on EM64T/Myrinet cluster
- CHARM/NAMD network problems on amd64 Clustermatic
- Charmm 1,4 Interactions - Scaling Question
- CHARMM compatible Methotrexate params
- charmm parameters for PEG
- charmm paramter
- CHARMM top and par files for PO4
- charmm toppology : internal coordinates
- Charmm++5.9 build on Mac OS X by IB xlc compiler
- charmm27 fatal error
- checking for correct construction of dihedrals, etc.
- Checkpoint on IRIX of namd 2.5 job not MPI enabled
- checkpoint software for NAMD?
- Class I vs Class II force fields
- cluster / scratch space
- clustering conformations
- Clustering of conformation
- clustermatic 4 and 5 Namd/charm
- Clustermatic and NFS mount
- clustermatic nodelist file
- CMAP
- CMAP and NAMD
- CMAP in NAMD simulation
- CMAP in NAMD?
- CMAP in VMD error
- CMAP problem
- collision correction of Locally Enhanced Sampling
- Combine pdb and psf files
- combine.tcl
- combined QM/MM calculation with NAMD
- command line arguments in NAMD ?
- command to run MPI and ABF
- Comments on 'restart' simulation
- Compilation of Charm++ on Linux opteron cluster with MPICH-GM installed
- Compilation of NAMD on 64-bit NUMA
- Compilation of NAMD on 64-bit NUMA with icc
- Compilation of NAMD on opteron cluster with myrinet
- Compilation problems on intel woodcrest
- compile "mpi" charm++ on amd64
- Compile charm++ with icc
- compile error on amd64 in src/ComputeTclBC.C
- Compile NAMD on Bluegene
- compile NAMD/CHARM on infiniband cluster
- Compiled NAMD on SGI Altix
- Compiling
- compiling charm++ with g++ 4.1
- Compiling charm++-5.9: Problems with g++
- compiling namd
- compiling NAMD on a redhat-pentium-dell workstation
- compiling Namd on amd64
- Compiling NAMD on AMD64 dual core
- Compiling NAMD with mpicc myrinet
- compiling NAMD: plugins
- Compiling on Linux-PPC970-Myrinet-MPI-xlC
- Compiling the NAMD on HPUX-ia64 system Error!
- Complementary programs for NAMD
- Complie NAMD on Suse Linux
- Compliling NAMD in RedHat9
- compute nonbonding interactions on bonded atoms
- computer network
- Computing cost of frozen atoms
- Computing Potential of Mean Force --SMD-cv
- computing resource
- concatenating two or more dcd files
- Condition for stopping MD sim. with NAMD
- conditional statements in conf files
- config files
- Configurational temperature - coordinates
- conformational alignment
- Constant electric field to selected atoms.
- Constant Energy Simulations
- Constrain only in Z direction
- constrain or fix the system only in Z direction
- constrained simulation
- Constraining a molecule and measuring the corresponding constraint force
- Constraining angles ??
- constraining center of mass-constrained MD
- constraining distance
- constraining water so that it does not get inside bilayer
- constraint constant in equilibration
- Constraint failure
- Continue a run ?
- Conversion for forces
- convert .dcd into .trr
- convert namd structure/coordinate files to gromacs topology file
- convert_from_namd_to_amber
- Converting Gromacs OPLS parameters to Charmm format
- CoordinateTransformation
- coordination chemistry with NAMD
- Correlation Functions
- corrupt dcd file >2GB on PowerPc
- Counterions: how to decide how many to put it?
- Counting H-bonds from a dcd file
- Crash during free energy calculation (MCTI)
- creating a pdb file based on sequence and psi phi omega values only
- cross products
- custom pulling path
- Data from Output file
- data structure of neighbor list
- DCD file
- dcd file format
- dcd file is too large
- DCD file really corrupt?
- DCD to PDB conversion
- define abf1 and abf2 for CM of water and CM of molecule
- deformations in a cubic water box during equilibration in NAMD
- deformations in a water box during equilibration in NAMD
- deformed water box after heating
- deformed water box during equilibration.
- density calculation
- Density of water
- density of water molecules in a water sphere
- deprotonated form of Proline molecule
- developing parameters for charmm
- Developing topologies for modified NA residues?
- dielectric constant
- difference between reassignfreq and rescalefreq in temperature controls.
- difference between two kinds of dimers
- difference in total energy values
- different cutoff for elecstrostatic and VDW interactions
- Different electrostatic and Van der Waals cutoff
- different result from different cpu
- Different solvents
- difficulties using SMD on atoms in large systems
- Dihedral and Improper, Nonbonded.
- Dihedral parameters for multiple minima
- dihedrals multiplicity in xplor psf file
- dissociation in NAMD
- dissociation of water
- Distance restraint
- distance restraints during a dynamic
- distorsion in hydrogens added
- dmpc membrane
- DNA protonation
- Do I need to use an xsc file to restart a simulation in NVT?
- Does NAMD calculate the potential energy of FIXED ATOMS?
- Dose restart frequently affect the results?
- DOWSER
- DPPC.Pdb
- DPPC.Pdb file needed
- dramatical standard deviation in the pressure profile
- dual core processors
- dublicated residue numbers in PDB/PSF
- dummy atoms and FEP
- Dummy particles
- Dumy atoms in FEP
- Duplicate lines in the output file !
- duplicated key CA in psfgen
- during namd build / compile -ltcl8.4 linking error
- ELECT energy
- electric field
- electric field and MISC
- electric field and MISC energy
- electron density profiles (EDP)
- electrostatics under spherical harmonic conditions
- energy
- energy calculation in VMD
- Energy due to electric field
- Energy for part of system
- energy minimization
- Energy Order of Magnitude
- Energy Plugin
- Energy Problem (Order of Magnitude)
- energy values
- ensemble
- equilibrated the system
- equilibrating the system with constrained Protein
- equilibration at three different temperature
- equilibration of protein
- Equilibration problem
- Equilibration with constant temperature and pressure
- Equilibriation Info
- errno = 2
- error about tclForcesScript
- error caused by atoms of lipid membrane
- error caused by lipid membrane
- error estimate in FEP calculation
- error in config file
- error in loading "import hessian/charge from single point calculation" in paratool
- error in membrane producing
- Error in running tutorial files
- Error in when using charmrun
- error message
- error message in free energy pert.
- Error on renaming file
- Error on Solaris
- error parsing config file
- error related to tcl boundary forces
- error running namd
- error using Namdenergy
- Error when running NAMD at SDSC
- ERROR: Constraint failure in RATTLE algorithm for atom 127!
- ERROR: Constraint failure in RATTLE algorithm for atom 598!
- ERROR: Margin is too small (BUG?)
- error: UNABLE TO FIND ANGLE PARAMETERS FOR C NH1 C
- Errors compiling NAMD 2.5
- Errors: Periodic cell became too small for original patch grid & Setting parameter binaryoutput from script failed!
- example scripts
- Expansion of DCD
- explicit hydrogen bonds
- extended system or Basis Vector
- external force
- extra lines in PSF !!!
- extra points in NAMD
- Extra terms in the expression for potential energy
- extracting time from DCDs
- extracting waters from DCD
- Factorization in PMEGridSize
- fad topology and parameter file
- Faltal Error. reassignFreq fails
- farnesyl&retinal
- Fat node
- Fatal error on PE 0> FATAL ERROR: DIHEDRALS INDEX 150255520
- Fatal error:
- FATAL ERROR: Asymmetric water molecule??
- FATAL ERROR: child atom 39 bonded only to child H atoms
- FATAL ERROR: DIDN'T FIND vdW PARAMETER FOR ATOM TYPE CAI
- FATAL ERROR: pairlist i_upper mismatch!
- FATAL ERROR: Stale NFS file handle
- FATAL ERROR: Tried to find atom type on node other than node 0
- FATAL ERROR: UNABLE TO FIND ANGLE PARAMETERS FOR CN7 CN7 CN7
- FATAL ERROR: unknown floating-point error, errno = 4
- Fe2+ parameters?
- Fedora Core 4 problems (?) ...
- Fedora Core 4 problems [2] ...
- fep
- FEP & different ligands
- FEP - one long simulation vs many short ones
- FEP alchemical
- FEP and solvent
- FEP and TI
- FEP charge perturbation
- FEP Energy very high: Mutual exclusion of atoms
- FEP error "atoms moving too fast"
- FEP error: Rattle atom constriant
- fep file
- FEP implementation in NAMD
- FEP implementation in NAMD - ERRATUM
- FEP in vacuum
- FEP output in NAMD
- FEP setup
- FEP, IONS, DUMMY atoms, LARGE numbers
- FEP....
- Ferric heme
- FFTW problem
- fix atoms in minimisation
- fix backbone atom
- Fix distance
- fixed atoms
- Fixed atoms and dcd file with DCDunitCell on
- Fixed restraint
- FixedAtomForces and ExcludeFromPressure
- Fixing atoms during simulation
- flexible cell for MD simulations
- flipDCD and Unit Cell information?
- Fluorophors ?
- Flushing output: MPI version of NAMD on AMD64
- follow up question about heating the system
- For help with .log file.
- force calculation
- force calculation during to conformational change
- force constant from gaussian to namd
- Force constant of harmonic restraint
- force constraints
- force over selection
- force shifted cutoff
- force-field parameters for TOAC
- forces calculation
- forming disulfide after equilibrating system
- forward and backward pulling
- Free Cluster-Building Workshops - 16-17 Mar 2006, 20-21 Apr 2006
- free energy calculate
- Free energy from MD Simulation
- Free Energy of Conformational Change Calculations Error: "Problem parsing input parameters Error: Invalid AtomID"
- free energy pertubation,binding energy and constant
- Free energy with amber topology
- Free Linux Cluster-Building Workshop - 30 Nov 2006 - 01 Dec 2006
- freeEnergy of conformational change of a test molecule
- Fwd: All or Nothing at All??
- Fwd: extracting waters from DCD
- Fwd: Fwd: Water Box size
- Fwd: GRADIENT TOLERANCE: nan
- Fwd: Parameter file.
- Fwd: Water Box size
- g(r)
- G5 cluster
- G5 clusters
- gcc4
- General question about NAMD
- General question about psfgen atoms.
- Generalized solvent boundary potential or similar tricks for huge systems in NAMD??
- Generate psf file of DMPC membrane
- Generating a lot of segments in proper order and selection around a center of mass
- Generating lipid bilayer model
- Generating psf for a drug, trimethoprim
- generation of non-standart charmm topology
- getbond (Tcl forces) / PBC
- getting #.IND #QNAN after phase 8
- Gigabit ethernet switch for cluster
- glucose CHARMM force field
- gradient for minimization
- gradient nan
- Gradient tolerance--total or per atom?
- gradually pressure change (increase/decrease)
- Gramicidin
- Gromacs parameters in NAMD
- H-H bond in solvate
- H-H bond in TIP3 water
- hanging at startup phase 0
- hard wall
- Harmonic Constraint: 2 types
- Harmonic restraints for moving residue positions??
- hbonds output!!!
- HD speed ??
- Heat Capacity & Relaxation Functions
- heat capacity: NPT vs. NVT
- Heating Up a system.
- help generating psf files
- 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 psf and par for small molecules
- Help with SMD
- 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
- HEME patch
- Hexagonal boundary conditions
- Hexagonal cell and PME grid.
- Hi
- hi ,everyone.I have a problem about random force
- hi all, I want to know how to turn the debug mode on of the namd
- Hi, call NAMD from C
- Hi,how can I generate a psf file with a pdb file contain some special amino acid like TYS
- hi...
- High VDW energies during minimization and dynamics
- high vdw energy
- HIS to HSD, HSE, and HSP
- histidine protonation
- History file of an ABF smiulation
- how add bond in psf file?
- How can I do protein complex's simulation?
- How can I increase the computing rate on the computer cluster
- How does NAMD calculate Electrostatic potential energy (no periodic boundary condition)?
- how gradually change (increase/decrease) pressure ?
- how is NAMD output written in parallel mode?
- how long is enough to heat up and equilibrate
- how long should the simulation be run
- How MD stopes at a specific distance?
- How to "extract" coordinates from a DCD trajectory file?
- how to add charged particles manually.
- How to append charmm stream file
- how to apply a random force on a atom
- How to atomselect several residues
- how to build AQP1 tetramer
- How to change psf file in the half way of VMD simulation?
- How to Compile NAMD on HPUX-ia64 system~
- How to conservate energy during NVE simulations???
- how to constrain a dihedral angle?
- how to constrain a dihedralqangle=3F?=
- how to constrains the smd atom on a line when do my smd simulation??
- How to contract the PBC cell
- 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 do free energy perturbation calculation in NAMD?
- How to get different kinds of harmonic constraints in one script?
- How to have neutral terminal ends
- how to image molecules back into a PBC box
- How to include more parameterfiles in NAMD
- how to install rmsdtt in Windows...
- How to make a disulphide bond
- How to make a virtual bond?
- 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 patch segments of aminoacids
- how to plugin catDCD into VMD of windows version
- how to plugin catDCD intoqVMD=20of=20windows=20version?=
- How to read charmm binary trajectory file using home-made C/C++ code
- how to remove translational and rotational motion from dcd file
- how to restart/continue NAMD run
- How to run for periodic boundary Conditions?
- How to run namd on NCSA Tungsten
- How to set a molecule to be rigid in NAMD?
- How to turn off electrostatic interactions (PME).
- How to use AMBER force field in NAMD?
- how to use gromacs force field in NAMD?
- how to use reaction field in NAMD
- how to use the dual-processor machines
- hybrid qm/mm
- Hydrogens collapsing
- Hydroxyproline topology
- I want to know how to make pdb file with 2d structrure file.
- IC Removal and Problem
- 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
- imprecision in table energy
- inconsistencies with amber force fields due to scnb and 1-4scalin g
- Incorrect periodic box imaging with AMBER parameters
- increase in energy over time
- Increasing temp during MD
- InfiniPath and NAMD
- infinite DNA
- infinite nanotubes with PBC in NAMD?
- Influence of PME grid size and cell basis vectors over simulation result
- Info: Adjusted background load on 11 nodes.
- inorganic surface peptide simulation
- input file for PO3
- Installation Problem
- Installing NAMD
- Installing NAMD on beowulf cluster, 64 bit, opteron, 4 processors.
- installing NAMD on opteron cluster with MPI
- Intel Woodcrest version?
- Interaction between metal and metal-water.
- interactions in flexible cel
- interactions in flexible cell
- Interactive Simulations, ligand size limits....
- interface with external program
- Interrupted system call
- Ion Channel Jarzynski
- ion concentration
- Ion-protein and protein-protein interactions
- Is clock skew a problem for charm++
- Is clock skew a problem for charm++)
- Is it equilibrated?
- is possible to remove the waterbox before running VMD
- Is the GBSA model in NAMD ?
- Is there a method to choose what is saved in DCD files
- is there any maximum limt of atom numbers in VMD or NAMD?
- isotropic pressure tensor
- Issue with rhombic dodecahedron / CHARMM compatibility
- It appears that the Claim that NAMD works with gromacs is false
- It is posible to allow Bond and angle degrees of freedom in tip3 water??
- it is posible to do NVE simulations in NAMD???
- Jump in Electrostatic Energy between two values
- Kinetic energy
- Kinetic Energy difference using restart binaries
- langevin vs coupling to a heat bath
- langevinHydrogen off?
- Large Box Sizes and Total Energies Observed in NAMD 2.6b1 Binaries of AIX-POWER-MPI and Origin2000-MPI
- Large energy fluctuation
- large vanderwalls energy during minimization
- last call for early registrations for "Horizons2005"
- LDB problem on Dual Atlon64 X2
- LDB question
- learning how to do a Cys palmitoyl patch
- LES
- les + conformational free energy
- LES / cLES
- LES : size
- LES and minimalization
- LES with PME and neutralizing charges
- libimf.so error when compiling charm++
- libimf.so problems
- ligands in VMD
- line too long in pdb file restart.coor
- LINE=*CMAP*
- Link Ammasso MPI with NAMD
- Linking with -memory paranoid
- linux cluster problems
- Linux HP Itanium Quadrics
- Linux-MPI binary of NAMD 2.6b1
- Lipid bilayer center go away from center of system.
- Lipid into NAMD
- Lipid membrane simulation by NAMD
- Lipids into NAMD
- load balancer, athlon 64 dual core
- loadforces problem
- Locally Enhanced Sampling
- log file
- log File - pressure not read
- long range electrostatics for alchemical transformation
- loodking or topology file for zinc finger
- make namd2 problem
- make the helix longer
- Manipulating structure
- many short runs or one long run?
- margin error message
- 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 problem
- MD Run frozen
- MD stops when COM or atom reaches a distance
- MDenergy error
- mDyne/A to kcal/mol/A2
- mechanical force calculation
- Megatest fails on Linux cluster
- Membrane configuration file
- membrane files
- membrane protein md protocol
- Memory requirements for clusters
- merge trajectory from NAMD
- Metal Ion and Protein binding
- Milestoning in NAMD
- Minimization after a MD simulation
- Minimization algorithms
- minimization of a cyclic peptide with NAMD
- minimization problem
- minimization temperature and constraints
- Minimization with NAMD
- minimize in FEP....
- Minimizing and Equilibrating
- minimum energy frame
- missing atoms in pdb file.
- missing info from NAMD output
- MM/PBSA
- MMPBSA...
- mmtools
- MMTools/PCA
- Modeling a polymer
- Modeling HCN.
- modeling sucrose
- modeling zinc binding site
- Modified DNA bases PDB files
- modifying cut off
- Molecular Dynamics or Langevin Dynamics
- Molecular Volume
- molecules distorted
- moments of inertia, principal axes
- more Heme troubles
- Morse potential?
- Mother atom with hydrogenGroupSize of 0
- mpi problems on opteron
- Multi Harmonic constrains
- Multimeric protein
- multiple automated calls to NAMD
- Multiple dihedral multiplicity
- Multiple Harmonic Constraints
- multiple jobs on a cluster
- multiple MD simulations
- Multiple residues at same position
- Multiple tclForcesScript
- Multiplicity of parameters
- munch: The input file main.o is not valid in the current object mode
- Myrinet NAMD
- Myrinet vs. Infiniband
- n terminal patch on proline
- N-methylacetamide
- Na ions got into the catalytic site during Production Run
- NAD splits up into 3 pieces
- NADP hydrogen zero
- NADP problem
- NADP topology
- NAMD & Gromacs FF
- namd + opteron/xeon
- NAMD 2.5 crashes unpredictably on a 8 way SMP (Linux x86)
- NAMD 2.6 in IBM SP
- NAMD 2.6 released
- namd 2.62b FATAL ERROR: Memory allocation failed on processor 0 or higher
- namd 2.6b1
- NAMD 2.6b1 error writing DCD file on Cray XT3
- namd 2.6b1 job crash error
- NAMD 2.6b1 released
- NAMD 2.6b1 Skipped Writing Velocity Restart File
- NAMD 2.6b2 on IBM POWER5 with AIX 5.3 Operating System
- namd 6-1- abf
- namd and amber force field
- NAMD and dual core Opterons, thoughts?
- namd and fftw
- namd and node freeze
- NAMD at NCSA
- NAMD attempting to read FFTW
- NAMD automation
- NAMD cluster run
- namd cluster run, connection refused
- NAMD compile in Mac OSX and IBM XL C/C++
- NAMD configuration files for NVT ensemble
- NAMD constraint force and energy
- NAMD crashes with LES option ON
- NAMD distribute
- NAMD Energy Plugin
- NAMD fails on Altix
- NAMD for inorganics??
- NAMD for Xeon clusters
- namd hangs
- NAMD hangs in parallel on OSX
- Namd hangs on Bproc cluster
- namd installation
- NAMD installation on Cray XD1 (AMD opteron 64-bit)
- NAMD installation on Xeon64 cluster
- NAMD is unstable on myrinet connecting cpus
- NAMD job abnormally killed with PBS
- 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 Myrinet issue - Strange behavior
- NAMD not starting calculations...
- NAMD octahedron
- namd on Altix
- NAMD on dual opterons
- NAMD on Dual processor computer
- NAMD on fedora 3 core?
- NAMD on IBM cluster AIX-RS6000
- NAMD on IBM pSeries (690, 655)
- NAMD on Intel XEON EM64T
- namd on lemieux
- NAMD on Linux IBM PowerPC JS20 Cluster
- Namd on Mac os X
- NAMD on myrinet
- NAMD on new P4
- NAMD on PSC
- NAMD on SUN
- NAMD on TeraGrid
- NAMD on TeraGrid: OpenMP?
- NAMD on Win64
- NAMD OSX Xgrid
- NAMD pairInteraction - huge VDW and TOTAL3
- namd performance on altix machines
- namd question
- NAMD recognizes only one MPI process
- NAMD restarts binary files
- NAMD results depend on # of processors!!??
- NAMD running only at 40-50% CPU capacity
- NAMD running problem
- NAMD simulation: HEME
- NAMD support for MNDO semi-empirical model
- NAMD time step: AKMA?
- NAMD timestep and numsteps
- NAMD to Amber
- Namd window network problem
- NAMD with Myrinet MX on MacOS X
- NAMD-2.6 Insatallation help
- 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/charm infiniband build
- NAMD/CHARM source installation option
- NAMD/iAPBS
- namd2 compile linux-i686-mpi
- namd2 mpi error
- namd2 on IBM P5 hangs
- namd2.5 on linux-cluster
- NAMD2.6b1 (&2.5) binaries on Scyld (missing libbproc.so.2 lib?)
- Namd2.6b1 FATAL ERROR: Memory allocation failed on AIX53 IBM-SP4
- namd2.6b1 hang on IBM p-690
- namd2.6b1 has bad scaling
- NAMD2.6b1 on an OSX cluster
- NAMD2.6b1 on MAC cluster problems
- NAMD2.6b1 on MACOSX
- NAMD2.6b2: Segmentation fault
- namd: adding water molecules
- namd: advice
- NAMD: compile problem
- NAMD: error messages
- NAMD: HEM residue
- namd: problem
- NAMD: run problem
- NAMD_2.6b1 shared lib problem on amd64 clustermatic using intel compilers
- NAMD_utilities
- namddat not working
- namddat: Command not found
- namdenergy
- namdenergy plugin
- namdplot error
- namdplot not working
- namdplot, graph is empty
- namdplot, grpah is empty
- namdplot: command not found
- namdstats
- namdstats gives nan's in tutorial output
- NANMD errors: PME, qsub
- Nanotube psf file.
- Nanotube simulation in water problem
- Nanotube Simulations
- NBFix and NAMD
- NBFix command to apply Lorentz-Berthelot mixing rules
- NBFix not working with charmm par file
- NDON! and NACC! in Parameter Files
- need pair interaction energies, not forces
- negatively charged proline as substrate
- net translation in long simulations
- New alchemical FEP tutorial
- new approach to counter FEP end-point VDW clashes
- New BioCoRE server released
- new problem
- NMAD job abnormally killed with PBS
- no Na or CLA paramters in par_all22_prot.inp
- no parameter for CN8-ON6
- NOE constraints with NAMD
- non-cubic boxes for Periodic Boundary Conditions
- non-repeatability NAMD simulations
- Nose-Hoover langevin piston pressure control and target surface tension
- Not getting good speed up
- NPT and FIXED atoms
- NPT ensemble with Periodic boundary condition
- Number of Steps
- nve ensemble
- NVT nose-hoover hamiltonian in SMD?
- Obtain message from MD
- one residue rmsd
- only minimization
- Only part of the protein is moving in MD simulation
- OPLS force field for carbon tetrachloride ( ccl4 ) ?
- OPLS-AA/L
- opteron 64bit installation
- optimisation for dual CPU sytem
- other crystal types in NAMD ?
- output in tcl
- output on Linux-amd64-MPI
- outputPressure
- OXT in pdb file
- Packaging 100 cations and anions in a box
- pair interaction
- pair interaction analysis of multiple trajectories with different timestep
- Pair interaction calculation for large number different pairs
- pair interaction cutoff
- Pair Interaction options
- pair interactions in NPT
- pair.pdb and cutoff for pairInteraction
- pairInteraction energies?
- pairinteractionSelf
- pairlist distance
- Pairlist warnings
- par_all27_prot_lipid.inp
- parallel NAMD output problem
- Parallelization method
- parameter and topology file for ethanol
- parameter and topology for 4-MI
- parameter and topology for cyclodextrin!
- Parameter file again.
- parameter file for DAD
- parameter file name
- Parameter file.
- parameter files
- Parameter files for Nanotube Simulation
- Parameter resetting in NAMD
- parameterizing novel molecule
- parameters for camphor
- parameters for NAD,NAG,NAP
- parameters for NVT ensemble
- part of a protein
- Partial charges for fluorescein/topology file
- particle access in tclBC
- Patch
- patch failed
- patch in psfgen...
- patch PYRT and extending DNA
- Patches & psfgen
- path problems
- pause simulation
- pbc_box
- PBS & local (scratch) space
- PDB files for carbon nanotubes
- Penetration of water
- peptide out of the water-box
- peptide simulation
- peptides confined in a water sphere
- performance differences on 2.4 vs. 2.6 Linux kernels
- peridic boundary condition
- Periodic Boundary Condition
- Periodic boundary conditions
- Periodic Boundary Conditions and Wrap
- periodic boundry conditions
- Periodic cell has become too small
- Periodic cell has become too small for original patch grid
- Periodic cell has become too small for original patch grid!
- periodic cell too small
- Periodic velcoity pulls
- phi and psi dihedral restraints
- phosphoserine
- pka calculations and their use in simulations
- please help-large energy change during FEP calculation
- plugins.tar.gz & charm_src.tar.gz !!!
- plz help!!
- PME for a hexagonal system
- PME grid error during minimization
- PME GridSize
- PME pair interaction analysis
- PME processors
- PMEGridSize
- pmf
- PMF Calculation
- PMF calculation using fixed restraints
- PMF error
- PMF force restraint question
- Poisson Boltzmann with NAMD
- polyethylene topology
- Poorly guessed coordinates
- POPC
- POPC or POPE?
- popc pressure profile
- positive VDW??
- Possible bug on NAMD 2.6B1?
- possible error warning
- Potential energies in TCL interface
- preparing a dimeric protein for NAMD
- preparing a dimeric protein for NAMD (Thank you)
- pressure
- Pressure -ve
- pressure calculation in applied field
- Pressure control
- pressure control in config file
- Pressure Driven flow of Water
- Pressure Profile Simulation
- Pressure tensor and periodic boundary condition
- Pressure_control
- prmtop reading error
- prob. with constraints
- problem about equilibration
- Problem about the energy change of refold of SMD protein
- Problem equilibrating with low pressure
- Problem heating the system
- problem in minimization while running
- Problem in restarting simulation
- Problem on NAMD simulation energy output
- problem reading topolgy files
- problem running namd
- Problem setting distance restraints
- Problem to run IMD simulation
- Problem using the GROMACS force field !
- problem using visual_mdenergy: program has trouble reading the dat file
- problem w/ free energy perturbation
- problem when do equilibration
- problem when heating the system
- problem while running NAMD
- Problem with Alchemical FEP
- Problem with biotin autopsf
- Problem with C++ libraries
- Problem with center of mass movement in simulation
- Problem with compiling NAMD on Suse 9.3
- problem with dihedral restraint
- problem with Dihedral Restraints
- Problem with equilibration and pressure
- Problem with mdenergy
- Problem with NAMD and constraint failures
- Problem with NAMD on Opteron cluster
- problem with PSFGEN
- problem with PSFGEN: the O3A atom cannot be recognized
- problem with reassigning temperature
- Problem with solvate and PSF files in CHARMM format
- problem with the NAMD CPU time consumption on a batch queueing system
- Problem with VMD 'animate' command
- Problems compiling NAMD on linux/clustermatic 5
- problems for runing NAMD on parallel computers
- problems NAMD_2.6 (fwd)
- problems of RATTLE with big systems
- Problems opening the Extended Trajectory File
- problems reading large dcd file
- problems with .conf script
- problems with autoionize total charge and minimization
- problems with paralellism
- Problems with the nodelist file !
- production in NVE ensemble after equilibration in NPT ensemble
- protein interact with its image
- protein is moving from center to one corner of water box.
- protein moves away from water box
- Protein moving out of PBC water box
- protein unfolding -- Phi MD
- protein/DNA complexes
- Protonation state
- Protonation state of HIS
- Protonation states
- PSC WORKSHOP: COMPUTATIONAL BIOPHYSICS WORKSHOP
- PSF file
- PSF file ATP
- PSF file format
- PSF file generation
- PSFGEN
- psfgen and charmm19: is there any inconsistency?
- psfgen and extending 5' end of DNA
- psfgen and poorly guessed coordinates
- psfgen error "Missing atom for conformation definition"
- psfgen for DNA
- PSFGEN for protein containing GTP
- psfgen gets ATP chiral atoms wrong
- psfgen operation for the C terminal of HSE
- psfgen patches
- psfgen problem
- psfgen trouble with heme
- Psfgen within NAMD
- psfgen/auto none
- psfgen: last CTER does not work
- ptraj
- Pulling of Center of Mass
- Qestions about NPT simulations.
- Qmeasure=22?= command
- qsub
- qsub on a linux cluster
- Queries on patches, GDP-topology
- question (fwd)
- Question about ABF
- Question about Constraint failure in RATTLE algorithm for atom
- Question about cutoff distance
- question about FEP calculation
- Question about free energy of conformation change
- Question about Generating DCD files with only specified atoms
- Question about load balancing
- Question about memory usage
- question about nonnbonded parameters
- Question about pair interaction feature
- question about par_all27_prot_lipid.inp
- question about patch
- question about protein leaving water box
- Question about REMD
- question about RMSD defined in NAMD
- question about the parameter "exclude"
- question about total charge change in FEP calculation
- Question about Van der Waals radii
- question on 1-4scaling factor
- question on free energy pert.
- 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 running NAMD2 using Amber files
- question on running NAMD2 using Amber files (fwd)
- Question on simulation energy output
- question on tcl script for rmsd calculation
- Question on the bond energy of NAMD tutorial
- question on the charged system
- question on the format of adding Lennard-Jones parameters
- Question regarding SMD
- question regarding the use of reaction coordinate "distance-com" in ABF method
- questions about anisotropic pressure coupling
- questions about applying patches
- questions about running namd on NCSA cluster tungsten
- questions about the use of HIS residue
- questions regarding output data of an ABF simulation
- questions regrading ABF
- radial distribution function
- Random forces in Langevin temperature control -- three questions
- random seed
- Rattle Algorithm
- RATTLE and DNA
- RATTLE Error
- Rattle Error During Equilibration of Lipid Bilayer Membrane
- RATTLE errors in equilibration
- rattle errors.
- RDF.tcl
- Re velocity error
- Re water box and system charge
- Re. Namd window network problem
- Re. van der waals energy
- reading a binary restart file
- Reading from DCD file and running MD
- Reassigning Velocities
- Recalculating energies from DCD file
- Recentering the box on target molecule and wraping
- recompiling NAMD 2.6 from sources on CentOS-3 x86_64: Charm++ failing test
- reconstruct PMF
- reconstructing backbone with psfgen
- reconstructing PMF
- redirecting stdout to a file
- reflective barrier
- Regarding box-size
- regenerating PSF file
- Regulating density of water
- relating FEP-derived ddG values to experimental IC50
- Remove water to close to the protein?
- removing a covalent bond during a simulation
- removing bonds in psf
- removing water from DCD
- Repeating again: Periodic velocity pulls
- Replica Exchange
- Replica-Exchange MD
- Report on a trajectory incompatibility between NAMD and CHARMM: Unfolding and RDFs
- Reproducing free energy profile for acetate-guanidinium association
- rescaling of coordinates in PBC simulations
- resetting restartfreq parameter
- residue name and segment name
- residue name LIP ... !
- restart a simulation
- restart problem
- restart syntax
- restart the simulation
- restarting a simulation accurately
- RESTARTING CONJUGATE GRADIENT ALGORITHM
- restarting SMD jobs
- restarting the simulation
- Restarting velocities
- Restartname
- restraining the protein not to move during equilibration
- return molecule to its principal axes
- Reverse Free Energy perturbation (FEP)?
- 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 other atoms
- Rigid bonds for United Atom Methylene Chloride CH2Cl2
- rigid protein
- rigidBond water
- rigidBonds water
- RMSD increases after restarts, decreases at the end of run
- rmsd is not stabilizing even after 0.6 ns
- RNA to DNA
- Rotating a structure about an atom
- rotating constraints
- rotation constraint angular velocity
- run frozen
- run NPT equilibration
- Runnig same config file many times
- running 2 jobs simutaneously?
- Running NAMD 2.6b1 on Linux Networks
- Running NAMD on a multiprocessor computer
- running NAMD on beowulf cluster
- Running NAMD on debug mode
- running NAMD on tungsten
- running NAMD2 in parallel
- running on two different machines....
- running VMD from a script?
- running VMD from a script? -- oops, never mind!
- same random numbers??
- saving coordinates as a PDB file after minimization in NAMD
- Saving coordinates of each frame into one separate .pdb file from a 100-frame .dcd file.
- saving picture from namdplot
- Saving the coordinates of DCD file in pdb format
- Scale
- scaling issue
- scaling NAMD2.6B1 on IBM P5
- scnb scaling factor and compatibility with AMBER force fields
- Script for calculating energy of a water molecule
- Script for MD in a loop?
- scripts for binding free energy calculation using SMD and Jarzynski's equality
- scyld no longer a supported option for building charm++ ?
- segfaults in mm_malloc
- Segment atom number limitation
- segmentation fault on Linux
- Segmentation fault with two processors
- Segmentation violation from APOA1 simulation on AMD64
- Segmentation violation in NAMD !
- segmentation violation!!
- Serious Steric Atom Clashes
- set center
- setenv: command not found
- setting configuration file for free energy perturbation
- Setting target minimization gradient?
- SGE (Grid Engine) on Rocks Cluster
- shake and minimzation, equilibration
- SHAKE or not?
- shape change of water box and peptide move out
- shmget error
- sialic acid
- simple query..
- simulated annealing
- Simulated Annealing Config
- simulated annealing step size
- simulated annealing with explicit water
- Simulating the orientation of detergent and lipid molecules around a membrane protein, bacteriorhodopsin
- simulation and equilibration
- simulation crashing with nan
- Simulation failed during the stage of heat
- Simulation Hangs during minimization
- simulation in nve ensemble
- Simulation in vaccum
- Simulation of a 1000 water molecules
- simulation of membrane-protein systems
- Simulation on AMD64 Dual Core - threads lose connection
- Simulation terminating due to RATTLE constraint failure
- Simulation with denaturants?
- simulations of periodic lattice
- Single point energy?
- Size of water box
- slow NAMD simulations on a AMD athlon64 in SUSE linux
- small query...
- SMD
- smd and loadforces
- SMD and restart
- SMD by pulling two groups apart
- smd dimer dissociation
- SMD Energy
- SMD From Force to Free Energy
- 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 temperature scaling
- SMD-drifting of center of mass
- Socket closed before recv.
- socket closed error
- solvate and write pdb, psf file.
- solvating a protein
- Solvent model other than TIP3 for use with CHARMM FF in NAMD??
- Some basic questions about NAMD
- Some problem on compiling NAMD
- Some problem on pair force calculation
- Some questions about TCL
- Some warnings from log file after minimization
- something about simulation of small molecules in NAMD
- sound velocity of water
- Space environment simulations
- SPC/E Water Model and RigidBonds
- Specific Heat Calculation with VMD
- Specific Heat Calculation with VMD]
- 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 ?
- steepest descent minimization
- steered molecular dynamics docking
- still on tcl boundary forces
- Still problems with heating
- strange behaviour when running apoa1 on 1 processor
- strange memory behavior
- Stretching Deca-Alanine
- Submitting jobs on myrinet...problem
- success with opteron myrinet mpi etc
- successive minimization with different sets of fixed atoms
- Superctitiacal CO2
- support TIP5? doubt on high temperature MD
- surface density of lipid bilayer
- Sybyl trajectory
- sync buffer overflow
- System after pressure change - confirmation needed
- system becomes very large when set LangevinPiston on
- system calls inside namd script
- System of POPC bilayer
- system rotates after equilibration
- target molecular moves away from water box
- Taurine parameters
- Tcl Boundary Forces
- TCL energy variables
- Tcl forces
- TCL forces and boundary conditions
- TCL Forces and Help on Script
- Tcl interface--dynamically changing simulation parameters
- Tcl parsing of NAMD config file does not work.
- tcl question
- Tcl scripting within NAMD configuration file
- Tcl, minimization and MD (Warning: I am a lazy ignorant)
- Tcl_Forces / 'loadcoords' loads NOT wrapped coordinates ?
- Tcl_Forces = pressure shifts while Langevin Piston is ON
- tclForces - addforce to group of atoms
- tcouple vs langevin
- tcoupling coefficient
- temp autocorrelation
- temperature "coupling coefficient" in NAMD
- temperature autocorrelation
- temperature coupling and pressure coupling
- temperature reassignment
- TeraGrid Efficiency
- Thanks a lot
- the "firsttimestep" conundrum
- The angle parameters for CN7 are missing in NAMD?
- the difference between the min_nacl.vel and min_nacl.restart.vel
- The HT-HT-OT angle parameter for TIP3?
- the lastest version of NAMD source
- the patch between segments for multiple chains molecule.
- the patching problem in psfgen
- The problem of "SMD and smd.tcl"
- The psf format conversion
- The vector direction in SMD
- thermodynamic integration and NAMD: soft-core or "separation-shifted" vdw potentials
- third time..can someone help!!
- Time of MD
- Timestep -- Can I use 2 fs timestep for 50 nanoseconds simulation?
- timestep in namd
- Timestep.
- TIP3P or TIPS3P
- TIP4P water
- TM protein in octane slab questions
- Tools to "open" domains
- top par for NAG, BMA ?
- topology & parameters for urea
- topology and parameter file for non aromatic nitrogen in ring system.
- topology and parameter for acetylcholine
- Topology file for Building Gramicidin A (tutorial)
- topology file with CT carbon
- topology files
- Topology for nano tubes
- Torque aplication with SMD
- total mol calculation
- Tpr
- Trajectory analysis
- trajectory extension
- Trajectory file.
- Transition path sampling
- Transition state
- TRIO
- tRNA simulation psf file generation explicit solvent and ions
- Trouble with Charmm/PDB?
- Trouble with NAMD on Myrinet
- trying to generate a peptide
- Trying to profile namd to look for memory leaks
- Turning off forces in VMD
- tutorial address
- two chain in pdb file
- two references
- two references- I got them, thank you!
- Type of force values in the tclForces script.
- Tyrocine dynamics came out wrong.
- UNABLE TO FIND ANGLE PARAMETERS FOR HT HT OT
- Unable to Generate PSF file !
- UNABLE TO OPEN .psf FILE
- unable to open charmm parameter file in Window
- UNABLE TO OPEN XPLOR PARAMETER FILE alanin.params
- undefined symbol errors:__builtin_bzero and _alloca building mpi-ppc-darwin version of namd2.6b1
- Understanding NAMD performance data
- unequal PMEGridSizes
- unexpected end with NAMD on quad-dual core opteron machine
- 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
- Unnatural Bond lengths
- Unprotonating GLU, ASP
- unstable simulation with AMBER ff in AMBER!
- unsubscribe
- unusual, periodic crash in Linux FC3/GM/MPI/CHARM/NAMD
- unwrapping dcd trajectory
- Update on Implicit Solvent Models in NAMD?
- Update on NAMD on BlueGene/TCL
- updating TCL version for NAMD?
- Urea parameter
- urestraint ?
- urestraint doesn't work
- urestraint for minimizations and MD (no PMF)
- Urey-Bradley term and VDW energy
- Use extendedSystem or cellBasisVector?
- UseConstantRatio between "run"
- useFlexibleCell
- useGroupPressure
- user defined restraints?
- Using an arbitrary tabulated potential in NAMD
- Using FEP as non-disruptive mutation procedure
- Using LES with AMBER parm files
- using namd to compute energies
- 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
- Van Der Waals energy
- variable cellOrigin
- VDW energy in CHARMM force field
- vdW parameters
- vdwGeometricSigma for OPLS in NAMD 2.6b1 Release
- vectorized NAMD version?
- Velocity after heating
- velocity error
- velocity error, still
- velocity file of atoms at each time step
- velocity quenching
- velocity unit
- Velocity unit ofvelocity in NAMD the binary files
- Vibrational mode analysis
- visualizing dynamics output
- VMD Command
- VMD scripting
- VMD scripting (Thanks a lot)
- VMD solvate in CCl4
- 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: autoimd on windows
- vmd-l: boubt about consistency of measures
- vmd-l: breaking the DCD file
- vmd-l: CMAP problem
- vmd-l: conformational alignment
- vmd-l: convert DCD files to CRD format
- vmd-l: CoordinateTransformation
- vmd-l: dummy atoms and FEP
- vmd-l: energy calculation in VMD
- vmd-l: error using Namdenergy
- vmd-l: force over selection
- vmd-l: Generating PSF for 1JNO.pdb chain A
- vmd-l: imposing period boundary conditions in a simulation with a crystal
- vmd-l: Interactive Simulations, ligand size limits....
- vmd-l: is possible to remove the waterbox before running VMD
- vmd-l: multiple automated calls to NAMD
- vmd-l: Multiple residues at same position
- vmd-l: namdenergy plugin
- vmd-l: Nanotube Simulations
- 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: ptraj
- vmd-l: script
- vmd-l: Script for calculating energy of a water molecule
- vmd-l: small query...
- vmd-l: Sybyl trajectory
- vmd-l: trace to newcartoon inconsistent display problem
- vmd-l: VMD Command
- vmd-l:namd-l; question about psfgen (param for CT1?)
- vmdtext and .cshrc.
- vmdtext?
- volume exclusion
- volume from VMD and NAMD different?
- Waiting for 0-th client to connect.
- wall clock vs secs/step metrics
- wallclock and cputime
- Warning in namd output file
- warning on unique coordinates
- Warning: 1 processors are overloaded due to high background load
- Warning: add bond failed in patch of ACE
- Warnings of psfgen
- water box and system charge
- water box and the procedure
- water box deformation
- Water Box Shrinks
- water density calculation
- water hole
- Water liquid-vapor interface
- Water outside protein surface
- Water simulation with namd
- Water Sphere
- waterbox
- what does "patch" mean?
- what does "syntax error" mean in VMD? and does confinment to some residue will cause error?
- What's the highest temperature I can go?
- What's wrong with my namd2
- 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 force field to choose
- why pressure is fluctuating so much
- why this error?
- Win64 version
- wrap ions
- writeback periodic cell info in dcd output
- wrong simulation times or misleading time counting?
- xplor parameter to charmm
- XPLOR psf format
- XPLOR topology to CHARMM
- Z-origin set to zero by Linux/Mac 2.5 binaries, Minimisation
- zero kinetic energy during minimization
- ZeroMomentum
- ZeroMomentum-Please help
- Zeros at the beginning of each line in the output
Last message date: Fri Dec 29 2006 - 23:10:16 CST
Archived on: Wed Feb 29 2012 - 15:42:59 CST
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