NAMD-L: By Subject
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About this archive
Starting: Tue Jan 02 2007 - 09:52:55 CST
Ending: Wed Dec 31 2008 - 05:25:21 CST
- "atoms moving too fast" error in bilayer simulation
- "binaryoutput no" doesn't work
- "CWeb performance data sent to wrong processor..."
- "Not all atoms have unique coordinates"
- "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
- (no subject)
- *** topology file for AMP? ***
- *.dcd and *.dcd.BAK
- , Build your vocab (word power)-Get emails daily Fr.ee
- ------------- Processor 0 Exiting: Called CmiAbort ------------
- .xsc file and .restart.xsc file
- 0 coordinates for LES atoms in pdb file after solvation
- 128 core namd job fails to run
- 128+ proccessor jobs on 64bit Widows hang upon completion of the simulation.
- 2 dimension PBC
- 2 molecule pair interactions
- 2 pdb files
- 2 proteins
- 2-D periodic boundary condition
- 2D periodic boundary condn & PME
- <no subject>
- =20=20How=20to=20compile=20NAMD?= 2.6 on core2 operons, x86_64-redhat-linux,which isqthe=20proper=20choice=20in=20Arch.?=
- =20=20nodelist=20being=20ignore?= d during paralleling
- =20?= qHow=20to=20compile=20NAMD2.6=20on=20core2=20operons,=20x86=5F?= 64-redhat-linux,which is the proper choice in Arch .?=
- =20How=20to=20build=20charm++=20on=20c?= ore2 processor
- _NAMD_crashes?= on winx64 during parallel run.
- A basic question?
- A difficult problem to explain the SMD force difference
- a philosophical question...
- a question about equilibrium
- A question about restaints force.
- A serious problem of NAMD output.
- a topology file in VMD
- A way to check for non-unique coordinates?
- abf "force not a vector" error
- ABF - changing the reaction coordinate
- ABF - PMF Calculation
- ABF - restricting reaction coordinate
- ABF - stretching deca-alanine
- ABF - using gyration
- abf - zeros as output
- ABF : dihedral-com.tcl
- abf and tcl scripting in NAMD
- ABF application
- ABF backbone dihedral
- ABF calculations
- ABF error calculation
- ABF fullsamples
- ABF inFiles
- ABF Method
- ABF or SMD
- abf output
- ABF Output File
- ABF parameters
- ABF question
- ABF restrain
- ABF simulations
- ABF tutorial; updated FEP tutorial
- ABF using distance-com but with negative xiMin
- ABF with different bin size
- abf: multiple distance
- ABF: split reaction coordinate in widows
- ABF:problems with calculating Free Energy Profile
- ABF:reversibility and number of samples
- Abnormal EOF found - buffer
- about 'loadforces' command...help!
- About Amber force fields
- About cutoff parameter for real space calculation in PME
- about force fields
- about normal mode analisys
- About para file format
- About pmf
- about PMF and MCTI
- About QM-MM
- About ref frame for rmsd vs time
- About RMSD
- about signal 11 received,exiting
- About smd
- abrupt deviation in rmsd values
- Acceptable pressure values
- Accepted temperature and pressure oscillation
- Access to CVS
- Acetaldehyde Dihedral Parameters
- AcetylProlineAmide topology
- add calcium chloride
- Add ions
- add Mg2+
- addforce on the com of a group of atoms and loadforces command
- adjusted background load
- affecting the atom velocities
- Alchemical FEP NAMD tutorial - problems with reproducing the results
- alchemical FEP question
- aligning ligands
- alkane-silicon_dioxide simulation
- all atom simulations with explicit water molecules and langevin thermostat
- all atom simulations with explicit water molecules and langevinthermostat
- AMBER ff99SB on NAMD
- amber parameters for congo red
- Amber PARM Input File Example?
- an aptamer and a lot of stupid problems
- angle deformation
- ANN: MDAnalysis 0.3 python library
- ANN: MDAnalysis python library
- Announcement: QM/MM Workshop
- Any flag values returned when executing "minimize" and "run"?
- Anyone have catdcd-4.0 for BlueGene?
- ApoB structure
- Appending dcd when restarting a simulation
- Appending to the existing dcd file after restart
- 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
- Applying SMD to a domain of protein
- applying stress to study elasticity
- Applying weak harmonic force between two proteins
- Approach energy with SMD
- Approach energy with SMD (2)
- April promo on watches
- Area per lipid.
- aromatic-aromatic interaction
- asphaltene parameters
- Atom velocities too high.
- Atoms mooving too fast ... still the problem
- atoms moving fast
- Atoms moving too fast OR constraint failure in RATTLE algorithm
- ATP molecule
- attractive harmonic potential between 2 molecules
- autopsf and hydrogen-sites
- Average energy in NAMD
- Average Velocity and How to choose Right Alias
- Avoiding alpha-helix distortions
- Avoiding self-interaction with PME.
- Backbone dihedral ABF
- bad exclusion error - searching remedies
- Bad global dihedral count.
- bad global exclusion count error
- balck box: what is the coupling constant when using langenvinFile?
- barostats in NAMD
- base stacking analysis of the trajectory of a nucleic acids simulation
- bash: namd2: command not found
- basic pdb file run with namd and vmd
- basic question about drawing methods
- Benchmark calculation
- benchmarking of NAMD: sustained performance (TF)
- Best NAMD version for Rocks 4.3 IBM xseries 3665
- BigDCD
- bilayer thickness in simulation of POPC membranes
- binary install question
- binaryoutput option doesn't work for dcd file
- Binding Free Energy
- Binding free energy by LIE
- biotin charmm topology/parameters
- Biotin-X charmm topology
- Bond energy become Zero!!!
- bond length in terminal patches
- BOUNCE namd-l@ks.uiuc.edu: Message too long (>40000 chars)
- bug in NAMD CVS starting March 7, now fixed
- build charm++ and namd
- build missing residues in pdb
- build smp version of namd with intel 10.1
- 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 NAMD 64-bit Mac OSX with GCC
- Building Namd on a linux cluster.
- building namd on CRAY-XT3
- Building NAMD on SGI Altix
- Building NAMD with Myrinet MX
- Building NAMD/CHARM++ Mac OS X Intel
- bunch of water molecules
- C NH1 C minimization error
- C1 splitting documentation
- C:CA bond getting stretched
- Calcium ion binding protein
- Calcium ion-Protein Binding
- Calcium ions and psfgen
- calculate interaction energies for a system with amber forcefield
- Calculating macroscopic properties
- Calculating PMF from a constant velocity SMD simulation!
- Calculation of CHARMM Parameters from GAMESS Output.
- Can I do ¡°accelerated molecular dynamics¡±in NAMD?
- can i somehow use reassigntemp for selected atoms only?
- Can I use "vecnorm" in the tclforce scripts?
- Can I use FEP in NAMD for reaction of ATP with Kinase?
- 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 the harmonic constraint parameters be changed between run or minimize?
- Can this be modelled in NAMD
- can we run EM of 2 or more proteins simultaneously
- Can you imagine?
- Can you satisfy your girlfriend?
- Can't find a good drug store?
- Can't stand sex all night long?
- cannot find -lsrfftw... collect2: ld returned 1 exit status
- Cannot spot error in namd config file
- Can´t use charmm to perform dcd analysis
- capping of end residues
- carbohydrates: CHARMM versus AMBER
- carma v.0.9
- catDCD 32 bit Vs. 64 bit Version
- CellBasisVector
- center-of-mass tcl and coordinate wrapping
- centre of mass fixed
- CFP: 3rd Annual CMM Workshop on QM/MM Simulations
- CG modeling using NAMD
- CG Name Prefix Problem
- CGMD parameters
- CGMD problem
- CGMD timestep
- change center of spherical BC during sim
- change in box geometry for simulation of pure water
- change segID using segment command in psfgen
- changing dcd output file DURING run?
- Changing loop to helix: restraining about 20 dihedral angles
- changing position of atoms during NAMD simulation
- Changing the protonation states of residues
- Changing the Secondary Structure of a Protein
- Characteristic time of atomic vibrations and collisions?
- Charges in NAMD topology file
- Charm compile: "xlC: command not found"
- charm installation problem
- Charm++ compilation
- Charm++ Fatal error ! Periodic cell has become too small for original patch grid!
- Charmm 22 vs Charmm 27
- charmm charge style
- CHARMM forcefield is free?
- Charmm format topology and parameter files for FAD
- Charmm is not free so how to learn it
- charmm parameter and topology files
- CHARMM parameters for H2S
- CHARMM partial charges and paratool
- charmm str file
- Charmm to Namd!!
- charmrun + NAMD on dual quad-core intel procs
- Charmrun and ssh problem
- Charmrun issues and namd on Win 64
- charmrun not found
- charmrun simulations over macpros
- charmrun socket error
- CHARMRUN vs MPI
- charmrun: execve failed to start; intel dual core Redhat
- checkpoint / revert
- child models little lolita lolita sex nude preteen girls preteen pics preteen incest sun bbs underage nudist sexy preteens bbs
- Cholesterol structure
- cis/trans prolyl
- clarification needed for wrapAll and wrapWater
- Classic timepieces replicas
- clustermatic 4
- CNT modeling
- Coarse grained model force fields
- Coarse grained psf file and parameter
- coarse grained simulation
- Coarse-grained Modeling/User defined FF
- Code question: Partitioning the patch contents into water and non-water
- COM restraint in NAMD
- combine pdb files
- combine PMF/dual FEP -> correct free energies?
- combining 2 dcd files into one
- 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 of the CVS code
- Compilation on IBM-Power (Linux)
- compilaton error
- Compile NAMD on Bluegene
- compile NAMD on Intel-64
- Compile NAMD on MIPS cpu(Loongson 2F)
- Compiling 8Core macs
- compiling charm++ failed on window with Cygwin
- compiling latest CVS on altix
- Compiling NAMD 2.6 from Source: no charm-5.9.tar
- compiling NAMD failed on windows with Cygwin
- compiling namd intel 9.1
- 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 namd on SGI Altix
- compiling namd2
- compiling namd: cannot find -lmodulecommlib
- Compiling Questions
- Complete Beginner
- config files no longer working after software 'upgrades'
- Configuration file
- Configurations-Statistical Mechanics
- conskfile
- const vel SMD
- constant velocity SMD
- Constant z axis
- Constrain centers of mass for selected atoms
- Constrain EVERY bond length and bond angle
- Constrain=?ISO-8859-1?Q? centers of mass for ?= selected atoms
- Constraining center of mass of monomers
- Constraint failure & velocity problem
- constraint failure in RATTLE algorithm for atom 3205
- constraint failure problem.
- constraints on zinc ions
- Constraints protocol
- constraintScaling - FOR LOOP
- Constructing a small molecule
- constructing a topology entry for hexadecane
- COntraints for lipid bilayer simulation
- Controlling the area per lipid
- convergence monitoring...
- convergence of abf
- Convergence of ABF calculation: n_samples
- Conversion of .dcd into .xtc format
- Converting a PSF file from one forcefield top another
- converting AMBER trajectory file to CHARMM trajectory file
- Converting DCD file to XTC format
- Converting PSF *BACK* to CHARMM
- COOH patch?
- coord file output minus solvation box
- Coordinates go to zero!
- Copper and Zinc: top_all27_prot_lipid.inp
- Correctness of Simulation Results
- corrupt DCD file
- Could I do the equilibration again with the same dcd file obtained?
- Coulombic virials
- Count protein solvent HBs?
- counting gas molecules inside the nanotube
- Crazy defoliator
- create inositol molecule
- Creating PDB from PSF and COOR files
- Creating topology for carbon nanotube / any new structure
- creation and equilibration of a monolayer
- Crystal Structure Analysis
- cubic periodic boundary box: what happen if I use a rectangular box?
- cyclic peptides
- Cyclopeptide: connectivity between the first and last residues
- dcd binary file format
- DCD file format
- dcd file produced with NAMD can be used with AMBER?
- DCD file size
- DCD for windows
- dcd to pdb conversion
- DCD trajectories produced by SMD simulation
- dcd trajectory format
- Defining a group of atoms in a simulation
- Deformations under constant strain rates
- DEN residue name in Amber
- Density Calculation
- Determining Equillibration of a membrane protein
- Determining Transition State from an Unfolding Simulation
- Did anybody really use TIP4P?
- Differences between 32bit and 64bit version of NAMD?
- different 1-4scaling values for different atom types?
- Different dcd files for minimize and MD
- Different Hbonds values on different machines using same script for same trajectories
- 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 coefficient from rmsd
- Diffusion of Protein through the membrane
- Dihedral angle calculation over the trajectories
- Dihedral coordinate ABF scheme
- Dihedral energy not getting generated ( is zero )
- dihedral force constant
- Dihedral Parameterization
- dihedral restraints "on-the-fly"?
- Dihedral restraints do not work
- Dihedral scan in NAMD?
- dimer minimization
- Direction of steered molecular dynamics
- distance constraints with an upper bound
- distance restraint w/upper bound example
- Dixitpd wants to Share Favorites with you
- DMF solvent parameters
- DMPC Atoms moving too fast !
- DMPC psf.
- DNA and low pH
- DNA H-bonds
- DNA helix model
- DNA hydrogen bonds
- DNA pdb file
- DNA simulation by NAMD
- Do we need to renumber atoms after solvate?
- Does anyone have a sample tcl file for counting H-bonds
- 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?
- Drift in performance
- drift in protein membrane simulation. membrane and protein one way, water the other way
- drop in Temp from NVT to NVE
- Dynamics with a glycerol molecule
- effects of box size
- Electron density profile?
- Electrostatics cutoff with PME
- electrostatics NAMD vs CHARMM
- EM and MD of GPCRs
- embedding protein in membrane
- Energy conversation
- energy drift in NVE
- energy minimization
- energy minimization help
- energy per residue
- Energy plot script
- Energy shift during simulation
- enery evaluation inside Tcl-Forces?
- entropy calculation
- eq. info.
- equilibration
- equilibration of "big" membrane
- equilibration of solvent box and pressure
- Equilibration simulation too slow.
- Error bad vdW format in Charmm parameter file
- Error compile charm++
- Error compiling NAMD with MPI
- error in atom type
- Error in equlibration
- error in explicit membrane protein simulations
- Error in NAMD Time Steps
- error message
- error messages in log file
- error messages with "reinitvels"
- error on installing ImageMagick
- error on running NAMD on a large cluster with prun
- Error on the constraints
- Error Parsing Config File
- Error while running NPT Simulation
- Error while using NAMD
- error with calling exec: child process exited abnormally
- Error with External Electric Filed module
- Error with Shape Based CG Model
- ERROR(S) IN THE CONFIGURATION FILE when running on a cluster.
- Error: Compile charm-5.9 on Fedora core 6?
- ERROR: Constraint failure in RATTLE algorithm for atom 872
- error: DID NOT FIND NIMPHI AFTER ATOM LIST IN PSF
- ERROR: DIDN'T FIND "NATOM" IN PSF FILE
- ERROR: Number of pdb and psf atoms are not the same!
- Error: parameter multiplicity.plz reply.
- Error: transport retry exceeded error
- Errors during equilibration: segmentation fault and bad global exclusion count
- errors in energy minimization
- Errors on Missing Atoms for Some Bonds
- experimental phi-values as restraints
- Explicit Membrane Protein Simulations in NAMD/VMD
- Extended System Conservation
- extracting coordinates from dcd file
- extracting forces from dcd files
- extracting interaction energies
- Extraction of force data
- failure in RATTLE
- failure in RATTLE algorithm using the adaptive biasing force method
- Famous repl1ca w4tches r0lex Cartier Bvlgari
- FAO developers: vdW energies, forces and derivatives
- Fast routines for distance evaluations using PBC.
- 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: chdir() failed!
- FATAL ERROR: DIDN'T FIND vdW PARAMETER FOR ATOM TYPE HN
- FATAL ERROR: DIDN'T FIND vdW PARAMETER FOR ATOM TYPE HT1
- FATAL ERROR: Patch needed for tuple is missing
- FATAL ERROR: Periodic cell
- FATAL ERROR: Periodic cell has become too small for original patch grid!
- FATAL ERROR: 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?
- Fe-S cluster topology parameters
- FEP + MCTI in one MD simulation
- FEP calculation of dimerization
- FEP configuration file
- FEP on charged residue mutation
- FEP output dEavg and dG
- FEP question
- Fep questions about FepEquilSteps
- FEP simulations?
- FEP triangular bracket average
- FEP: delta_G, memory of Hamiltonians corresponding to last G value?
- FEP: FATAL ERROR: Periodic cell has become too small for original patch grid!
- FEP: How check equilibration sufficiency? calculate dG?
- files for air
- filling hydrophobic cavity with... methane?
- finding free energy at a time step using abf
- Finding size of water box
- first aid
- firstLdbStep and ldbPeriod
- firsttimestep question
- fixed atoms / pressure
- fixed atoms appearing on the other side of simulation box
- FIXED atoms not included as described in the documentation
- fixed residue
- fixed system just in Z direction
- fixedAtoms may not be enabled in a script
- fixing internal coordinates
- flexiblecell and constant ratio
- fluorescent probes
- Flying ions
- For slowly heating, temperature reassignment or Temperature coupling
- for the isntall and run NAMD soft on 8 core (dual quad-core Xeons) system
- Force Calibration Interaction
- force constant for zer-velocity SMD
- 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
- force field parameters for fullerenes
- force on SMD atom
- force potentials for residue-based CG
- force-field parameters for glycoproteins
- forces on atom
- Format of Binary Restart and Output Coordinate and Velocity Files
- Fortran and tclForces
- Free energy calculation fixing the dihedrals
- free energy calculations
- Free Energy of Conformation Change
- Free Energy of Conformation Change Units
- Free Energy of Conformational Change PMF - documentation on method?
- Free energy perturbation of a double mutant
- free energy,energy,entropy calculation for pushing ATP to active site of kinase!
- Free Energy/ ERROR
- free enrgy calculations - an additional information
- Freezing point
- from NPT to NVT
- Full Electrostatic Calculations on Protein in Vacuo
- FullSamples variable in ABF
- Fwd: convergence of abf
- Fwd: Determining Transition State from an Unfolding Simulation
- Fwd: How can I load two forcefied at the same time
- Fwd: Laptop for Molecular Dynamics - Summary
- Fwd: namd2 installation..
- Fwd: regarding protein-dna complex simulation please reply.......
- FYEO
- g(r)
- g(r) plugin
- Gas phase minimization
- general question on protein-membrane simulations
- general question on protein-membrane simulations -complete message!
- generalized born routine
- Generating a gromacs topology file for analyzing NAMD trajectories
- generating psf & energy calculation for unusual amino acid - Aib
- Generating PSF from modified AMBER ff
- Getting density of water..
- Getting total energy of system + pressure and temperature bath.
- Globus-WS Submission of a NAMD Job ..
- GPU acceleration press
- gpu pressure control
- Grand canonical ensemble
- guesscoord fails, hydrogen adding problem, output pdb is all zeros
- H-bond energy
- H-bond occupancy in nucleic acids
- Happy Viagra
- Harmonic dihedral restraints
- harmonic distance restraint
- harmonic restraint between two atoms
- has anyone patched NAG to ASN?
- heat diffusion
- heat diffusion calculation
- Heat flux along CNT
- heat flux when using langevin dynamics
- heating system
- heating with restraints
- Help
- Help !!! ERROR: Atoms mooving too fast
- Help Needed>Compiling source namd mpi enabled for a linux cluster
- Help reg. input file
- help regarding NAMD equilibration
- help with calcforces
- help with TCL forces script
- Help with TCl script
- help! How to build charm++ on core 2 computer processor
- help!!
- Help: do you have the top parameter of Gla
- hexagonal box
- hexagonal crystal
- Hi,Thank you!
- High background load warning message
- Hoe to create psf file of C-terminous of protein?
- How can I calculate the distance between two atoms frame by frame?
- How can I get parameters of unknown residues
- How can I monitor the force during constant velocity SMD?
- How can I set Tcouple ?
- How can I specify an exact initial velocity?
- 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 do you debug tcl scripts in vmd ?
- How do you evaluate forces on a fixed atom?
- How do you keep atoms a fixed distance apart?
- How does NAMD count atoms in PDB files?
- How is the maximum velocity limit set?
- How to "twist" a molecule?
- How to "twist" a molecule? (resubmit)
- How to access energies after MD step with Tcl ?
- How to analyze? Namdstats, namdplots, etc.
- how to apply different damping coefficients simultaneously to different atoms in the same system.
- how to apply restraints for phi and psi for alpha helix regions
- How to apply velocity to the entire system with COMmotion enabled
- How to 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 choose force field?
- How to circumvent: FATAL ERROR: Periodic cell has become too small for original patch grid!
- How to compile NAMD2.6 on core2 operons, x86_64-redhat-linux,which is the proper choice in Arch.
- How to compute interaction energies between individual amino acid residues
- How to construct .prm file of phospho-THR?
- how to convert dcd files from namd to charmm
- How to define a spatial grid for a temperature landscape/contour
- How to evaluate the area per lipid and thickness of a lipid bilayer?
- How to fix atoms during minimization?
- How to fix the Center of mass of protein when performing SMD?
- How to freeze some atoms
- how to generate psf file using the AMBER topology file
- how to get 2 identical trajectories using NAMD in parallel
- How to get around with "atoms moving too fast"
- How to get over with the error "Atoms moving too fast; simulation has become unstable and Exiting prematurely.
- how to get the velocities from the dcd file
- How to implement an additional interaction potential?
- How to include parameters from stream files in calculations
- How to install VMD and NAMD on Ubuntu?
- How to keep Total Energy constant when an external force is added?
- 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 alkaline ph pgn file
- how to minimize the energy of a protein using CHARMM FF in NAMD
- how to perform MD with two proteins
- How to play molecule trajectory with VMD?
- how to prepare *.paramas file
- How to read specific DCD frames directly in Fortran?
- How to restart a simulation
- how to restart FEP
- how to restart/continue NAMD run
- How to retrieve IC50 of a specific compound from NCBI?
- How to reverse the smd pcv pulling simulation
- how to run namd in cluster
- How to run namd2 on ubuntu linux?
- How to run NVT simulations without applying periodic boundary conditions?
- How to save the animation movie into files?
- How to save vmd figures to jpg or tiff?
- How to set values for cellBasisVector and PMEGridSize properly
- how to simulate sugars
- How to unsubscribe ?
- How to use bigdcd on a trajectory while skipping first 1000 frames
- 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 the transformation matrix in VMD to obtain the tetramer
- How to write a new dcd.file by using Tcl
- How to write different DCD files for separate MD runs in one simulation?
- How to write gradual heating config file
- howcan I use amber forcefield in NAMD?
- Howto lengthen a collagen strand (which tool to use)
- HP Cluster Platform 4000
- HP-MPI on Xeon Infiniband
- HSE and gromacs
- Hydrogen Atoms and Water Molecules
- Hydroxylysine parameters
- Hymen destroyer
- Hymen penetrator
- I'm sorry ... please ignore the junk !!
- Implementation of TCL script in NAMD .conf file
- implicit solvent energy calculation
- Implicit solvent simulation
- Impressive Glashutte timepieces
- improper torsion
- impropers for aromatic residues
- Impropers in histidine residues
- Improve your sexual life and save up to 80%
- Inconsistencies in NAMD simulations
- Incorrect Atom Count
- Incorrect PSF file for min.pme
- Increase the decimal points of energy output
- Inexpensive IWC watches
- Infinite Armchair Single Wall Carbon Nanotubes and Periodic Boundary Conditions (PBC)
- infinite layer
- Initial and final state fix MD
- Inorganic Builder Plugin
- Inquire on gradual temperature increase.
- install namd on dell power edge 1900
- install NAMD on Ubuntu
- install VMD on Ubuntu
- installation of charm-6.0 in ia-64 cluster machine
- Installing NAMD
- Installing NAMD 2.6 on SMP machine... charm++ install errors
- Interaction energy
- Interrupted system call
- intramolecular LJ parameters
- Invalid cpus 2 in nodelist ignored
- ionize (big, big, big system!)
- ions behavior in protein-water box:
- Is it better to align all the trajectory before calculating rmsd?
- Is it possible to compile NAMD win64 with MPI (windows MPI)
- is there any informatn on callback??=
- Is there solution to numerical inaccuracy
- Is very slow heating "bad"?
- It doesn't work with using amber files.
- Itanium_and_CMAP
- job stall w/ incresed cpu usage
- Just can't seem to compile charm++
- Kinetic Energy frm MDEnergy (energy evaluation tool)
- Kinetic Momentum of Translation and/or Rotation
- langevin dynamics
- langevin dynamics and random seeds
- langevinDamping
- langevinHydrogen off with rigidBonds all?
- langevinHydrogen off with rigidbonds off?
- LangevinTemp and KE calculation
- Language Used and Elementary doubts
- Laptop for Molecular Dynamics
- Laptop for Molecular Dynamics - Summary
- Large Benchmarks
- Large MD simulations and atom number limits with NAMD
- Latency vs Bandwidth over Infiniband
- length of an ABF simulation
- libstdc++.so.5
- Ligand Bound.
- ligand parameterization
- ligand parameters... I know the next step
- ligands parameters
- Light dummy atoms (source code question)
- lithium parameters
- lj parameters for gold for NAMD
- load balance strategy query
- Load balancing off
- load balancing question
- Loading .vel file in VMD
- loadtotalforces error
- lock / unlock threads
- log file problem
- looking for paramter
- Loops in tclForcesScript
- MacOSX 64bit binaries
- MacOSX net version segmentation fault
- Maestro Penis
- Managing Log files
- Margin Error
- margin value
- Maximum Velocities
- MD analysis
- MD for phospho-aspartate using NAMD
- MD of DNA
- MD performance on 10 GBit/s or 20Gbit/s infiniband
- MD problems
- MD runs at different clusters
- MD-problems-GPCR in POPC bilayer
- Meaning of lines in "run" part of log file.
- megatest test failure/MPI problem
- Membrame Volume Increasing after restart
- membrane
- membrane constraints on thickness
- Membrane potential
- Membrane Protein Simulation Problems
- membrane simulation: pressure control parameters
- Membrane Simulations
- membrane using OPLS force field
- Membrnae (POPE)/protein simuliation.
- memory overflow problem of Tcl scripting when dealing with trajectories
- merge dcd files ,catdcd
- Mindboggling Problem Related To NAMD2 Code
- minimization
- minimization and MD in one configuration file?
- minimization command
- minimization error - high IMPRP energy
- minimization of the squared gradient
- Minimization using Fixed Atoms
- minimization warning and errors
- minimization with amberff
- minimization-problem
- Minimizer
- minimizing bad system: bad global excl. count
- minLineGoal comannd
- mismatch of topology with parameter file
- MM works MD does not in Fixed system
- Modification of the NAMD forcefield functions ???
- modified patch to PROline
- Molecule drifts and high average RMSD per residue
- molecule leaves water box during md
- molefacture in vmd
- monitor a distance between two molecules
- Monte Carlo with NAMD
- MPI compile of NAMD runs on dual core machines but not quad core machines
- mpirun compilation for NAMD
- Multiple constraint file
- Multiple Different Harmonic Restraint Defitions
- multiple simulations
- Multiple successive addforce calls
- multiple tcouples?
- multiple time stepping in namd: Query
- multiple timestep and dcdfreq
- multiple topology files
- Multiplicity of Parameters
- Multiplicity of parameters for improper bonds .............. of 1 exceeded.
- mutate G->U?
- my simulation dont be minimized when I fixed the channel
- NAD topology and parameter file
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- NAMD & CUDA, still in development ?
- NAMD + nice
- NAMD + TMD on Abe
- NAMD - Pronunciation?
- namd 2.5 compilation error
- NAMD 2.6 - PME Error on Large Protein-DNA System!
- NAMD 2.6 dcd and breaking XPLOR
- namd 2.6 installation on i686 problems
- NAMD 2.6 installation problem
- NAMD 2.7
- NAMD 2.7?
- NAMD binaries
- NAMD Carbohydrate Simulations
- NAMD cg configuration file
- NAMD compilation / TACC Ranger
- NAMD COMPILATION ERROR
- NAMD compilation on linux cluster
- NAMD compile error
- namd crash: Signal: segmentation violation
- NAMD crashed with TclForce turned on
- NAMD crashes on winx64 during parallel run.
- namd cvs compilation
- NAMD CVS Installation
- NAMD CVS RUN ERROR
- NAMD electrostatics no cutoff or switching
- namd energy
- namd energy self interaction reality check
- NAMD fails with LAM (can't run example)
- NAMD for Intel Xeon Cluster with MPICH
- NAMD hangs at "OPENING EXTENDED SYSTEM TRAJECTORY FILE" / PME error
- NAMD in Solaris X86
- NAMD in water vs in vacuum
- NAMD install problem.
- NAMD Installation - SUSE Linux 9.1 on IBM X Series 335
- NAMD Installation Problem
- NAMD Integration algorithm
- Namd job terminates after ~10000+ itrations
- namd latest CVS version on BluegeneP
- namd linked to tcl8.5
- NAMD log file analysis script problem (namdstats.tcl)
- NAMD mail bounce problem.
- NAMD message
- namd mpi version with smp
- NAMD on a remote UNIX and VMD on local Windows - does this work?
- NAMD on Abe
- NAMD on blue gene BG/P
- NAMD on CELL BE
- NAMD on dual core, dual processor machine?
- NAMD on dual quad-core Xeon's with Infiniband backbone
- NAMD on Infiniband - problems and successes
- NAMD on Power5
- NAMD on RedHat Linux
- NAMD OUTPUT
- NAMD Parameter File Creation
- NAMD plot plugin
- NAMD question
- NAMD run
- namd seg fault on Intel cluster
- NAMD Simulation error
- NAMD stops running without error messages or termination
- NAMD Timestep
- NAMD to CHARMM unit cell information in DCD
- NAMD trajectory format
- namd vs gromacs vs charmm vs amber
- NAMD vs. CHARMM. Is complete correspondence possible?
- Namd water density
- NAMD with CUDA Status ?
- NAMD with mpirun
- NAMD+MPI on AMD64
- namd-l : Topology info - RESidue information for carbon nanotube
- namd-l-outgoing2@halifax.ks.uiuc.edu
- NAMD-L: autoionize error
- NAMD-lite - Heun's method implementation
- namd.conf with OPLS options
- NAMD/Infinipath installations
- namd1 - abf analysis
- namd2 erratic performance over 104 procs
- namd2 installation..
- namd2 run error
- NAMD2.6 appears to be freezing at or during load balancing
- NAMD2.6 repeatedly freezing on new desktop
- NAMD2.6 requirments on p690
- namd: 64 p job runs; 128 p job fails why?
- namd: ABF query
- NAMD: constraints while heating
- namd: DSPC and DAPC for a phospholipid bilayer
- NAMD: Exiting Prematurely
- namd_minimize
- namddat
- namddat syntax error
- NAMDEnergy
- NAMDenergy + PME for constant pressure trajectories (variable box and .xst files)
- namdenergy and amber trajectory
- namdEnergy gives significantly different values from those in log file?
- NAMDENERGY in parellel
- namdenergy strange behaviour !!!
- NAMDENERGY: function of 'cutoff' parameter when -pme option is enabled
- namdplot Unmatched " error
- Nanopore simulation
- NCSA Abe versus TACC Lonestar
- need help on CG modelling
- negative force
- Negative Pressure
- Net charge of the system is not zero
- Neutral arginine patch in topology file.
- New ABF order parameters
- new spam filtering
- NNB in PSF and alchemify
- No effect of periodic boundary conditions?
- no effect on velocity scaling
- Nobody will know about your problems.
- nodelist being ignored during paralleling
- Non Bonded Paramters
- non-parallel NAMD compilation
- Non-standard amino acid
- nonbonded interactions
- nonbonded interpolation
- Normal mode analysis
- NPT enzemble and ABF
- NPT_NPgammaT_or_NPAT_for_membrane_with_CHARMM_forcefield
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- Number of atoms to high for mdenergy
- NVE ENSEMBLE
- NVE ensemble configuration file
- nvidia and namd
- NVT simulation by NAMD
- NVT/NPT pressures w fixed particles
- Oligomer
- One question about running NAMD
- One Year written repl1ca w4tches warranty
- OPLS dihedrals
- OPLS force field in namd
- OPLS Lipid topology/potenital for NAMD
- OPLS-AA toppar files
- Orgasm power
- Orgasmotron
- output .coor minus solvation box
- output area
- Output force acting on each atom in the system
- Output of forces.
- output while tclforces active
- Overlaoded processors when running NAMD on NCSA Altix
- OXT in pdb file
- pair interaction
- Pair Interaction Calculations to get Charmm Charges?
- Pairinteractions
- pairlist i_upper mismatch!
- palmytoilated
- par-extraterms.inp file needed
- parallel execution speedup
- Parallel performance on Intel Woodcrest
- Parallelism issue
- Parameter
- Parameter file for Gold ?
- parameter file to make cholesterol psf file
- parameter for compiling
- Parameter or patch for thioester
- parameterizing a beta aminocyclohexanecarboxylic acid
- Parameterizing ligands with protein
- parameters and topology file needed for coarse-grain simulation
- parameters for GABA (gamma-amino butyric acid)
- Parameters for NH3, NH4+, and CO2
- paramter
- paratool for MG
- Partial charges on amino acids
- patch DISU to 2 residues
- patch LINK - cyclizing a protein
- Patch needed for tuple is missing Error with POPC bilayer
- pbc
- PBC related query
- PCA calculation
- pdb file
- PDB residue renumbering
- Penis Launcher
- peptide conformation search examples
- Performance Problems on Linux Cluster / Bad Scaling
- Periodic BCs
- Periodic boundary conditionds-Surface Energy
- Periodic boundary conditions
- Periodic Box Size vs. Water Box Size
- periodic cell conditions for membrane simulation
- Periodic Cell error on CO2 MD
- periodic cell has become too small for original patch grid!
- Periodic Run Crash
- pH in NAMD
- phi and psi restraints for 2 helix regions
- phosphate (PO4) topology
- phosphohistidine parameters ???
- Platinum paramaters
- Please unsubscribe me
- PME and infinite polymer
- PME and r-RESPA issue in NAMD
- PME fails no matter what
- PME Grid Size - how far to deviate from cell basis vectors.
- PME non-zero charge
- PME on a negatively charged system
- PME on a negatively charged system.
- PME questions
- PMEGridSize
- PMF
- pmf calculation
- PMF calculation floating-point error
- PMF of SMD using CHARMM generated trajectories
- pmf segname for amber ff. MAIN?
- PMF, defining end point
- PO3 psf
- Polarizable force fields
- POLL: free energy of conformational change
- POPC bilayer- System size
- POPE/protein simuliation.
- Postdoctoral Position in Scientific Computing
- Potential function (force field) in NAMD
- Potentials of mean force using ABF
- Power penis
- Premature stop
- Prescr1ption med1cations... without a prescr1ption!
- pressure calculation
- Pressure calculation method
- Pressure Discrepancy
- Pressure fluctuations
- Pressure oscillation in NPT
- Pressure problem when using restart file
- Pressure related issue
- pressure vs density tip3p
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- printing and global variables within TclBC script
- Problem about cellBasisVector
- Problem about momentum correction
- problem about pairlistdistance...
- problem building Namd frm source...
- Problem compiling NAMD on BlueGene
- problem compiling NAMD2.6 in a MacOSX-PPC
- Problem en equilibration Protein into a bilayer membrane POPC
- Problem for to use/compile NAMD with mpiexec
- Problem in energy conservation in NVE ensemble with 1fs timestep
- Problem in making cyclic peptide
- problem in NAMD minimized structure when viewed in VMD ramaplot
- problem in running equilibration
- Problem in Running namd2
- problem in solvating the protein
- Problem regarding psfgen
- Problem while installing NAMD
- problem with *.pdb and *.psf
- Problem with .conf file of NAMD
- problem with ABF "can't read forces(80)"
- Problem with creating psf file from structure made by inorganic builder
- problem with executing MPI program in NAMD simulation
- Problem with NAMD crashing without warning or error messages
- problem with NAMD RNA run
- problem with namddat_unix: Plz help...
- Problem with NVE run: Help
- problem with periodic boundaries
- Problem with TclBC when run in more than one processor
- Problem with temperature increase in equilibration.
- problem with VMD installation- libstdc++.so.5 => not found
- Problem with water box
- Problems compiling NAMD
- problems compiling NAMD on SCALI architecture
- Problems found --- [Fwd: Bad global dihedral count.]
- Problems of mpi with namd 2.6
- Problems on SMD simulation
- problems replicating a DOPC membrane
- Problems restarting an amber simulation
- problems running more than 9 Replicas in replica exchange simulations
- problems running Replica Exchange simulations using SSH to spawn the processes
- problems sourcing namdstats in vmd
- Problems with (Restrained) TMD in NAMD
- problems with combine.tcl
- Problems with CUDA Build
- Problems with energy conservation in NVE dynamics with 2fs timestep
- Problems with minimization
- problems with mutation in psfgen
- Problems with Mutator1.1, mutations and FEP
- Problems with the charge (membrane simulation)
- Problems with TMD could not be solved with the CVS version
- Problems with using multiple Tclforces scripts sequentially
- Problems with version 2.6 for amd64
- problems-periodic cell
- Products that can improve you life!
- protein diffuses to boundary..
- Protein hydrogens causing "Atoms too fast" error
- Protein in/out of box
- protein instability
- Protein moving out of water-box after 10 ns simulation
- Protein partially denatures during pulling
- protein spinning and total enegy not constant in NVE
- PROTEIN VACUUM MINIMIZATION ERROR
- Protein, ligand, ion out of the water box.
- protein-DNA complex
- protein/lipid simulation
- protein_RNA simulation
- Protonation of nucleic acid phosphates in CHARMM for use in NAMD
- protonation of some histidine residues
- psf file
- psf gen
- psf generation for a small non-peptide molecule
- psf generation for a small non-peptide molecule - again
- PSF of Tryptophane methyl ester
- psf-generation.
- psfgen
- psfgen and bond topology specification
- psfGen error
- psfgen for pre-equilibrated membrane bilayer
- PSFGEN Warnings about H positions on standard amino acids
- psfgen: merging of 2 dna chains
- psfgen: more problem
- psgfen patch
- ptraj
- ptraj --- 2drms
- puase MD integration to communicate between jobs
- pure TIP5P water system with AMBER7 parameters
- Push ATP to active site of kinase!
- python vs tcl
- Q=D4=D7=C5=D4:__128+_proccessor_jobs_on_64bit_?= Widows hang upon completion of the simulation.
- Quantitative Test for Equilibration of Data Time Series
- quartz / FF(Lopez&MacKerrel)
- quartz slab / pairInteractionSelf / Bad global exclusion count!
- query about thermostat..
- query about wrapped coordinates
- query about wrapped coordinates: Problem SOLVED
- Query Regarding FEP tutorial: NPT or NVT?
- Question about 'NAMD TUTORIAL'
- Question about a shift in rmsd using fixedatom off
- Question about ABF
- question about ACE and NME patch
- Question about catdcd and DCDunitcell
- Question about compiling NAMD
- question about equilibration step
- Question about Error Message
- question about the influence of water box size in FEP
- Question for 2D periodic boundary condition
- question on ABF
- question on heating
- Question on SMD simulation in spheric water .
- Question regarding ABF simulations
- Question regarding NAMD nonbonded routines
- question regarding nearest-image resolution in NAMD
- Question regarding SETTLE (RigidWater)
- question related to rmsd
- question switching function
- Questions about equilibration
- Questions concerning NAMD
- RAM/node
- RATTLE algorithm error
- Rattle Error
- RATTLE error and GROMACS parameters
- RATTLE failure
- RDF.tcl question
- Re- Loading .vel file in VMD
- read dcd binary trajectory
- Reading and writing Binary Restart or Output files with Fortran
- Reading multiple .log files
- Reading multiple .log files into one
- Reason: FATAL ERROR: Simulation config file is not accessible.
- Reassign temperature for selected atoms?
- recalculating energies
- recalculating energy using dcd file
- recenter atom and remove rotation (translation)
- Recommended solvation box size
- reg parameter of ions
- regarding cgmd
- Regarding Installation
- regarding protein-dna complex simulation
- regarding protein-dna complex simulation please reply.......
- Regarding REMD
- Regarding Trajectory analysis
- regarding writemol2
- relating to NAMD Energy Plugin scripting
- REMD
- REMD using PBS qeue
- removing waters from big dcd files
- Replica Exchange (Parallel)
- Replica exchange error message
- Replica exchange MD
- Replica Exchange MD using Amber parameters
- Replica Exchange Method
- Replica Exchange NAMD
- replica exchange trajectories
- Replica Exhange error: POSIX EINTR {interrupted system call}
- Replica or Original?
- Replica Server Tutorial
- replicating a DOPC membrane
- replies
- Report
- reproduciblity between software
- Residue name for Dimethyl sulfoxide
- residue_rmsd.tcl question
- resonable dcdfreq
- restart
- restart a NAMD simulation after coordinate transformation in VMD
- restart a NAMD simulation after coordinate transformation in VMD (solution)
- restart NAMD job
- restart PMF calculation: what is "lambdaRef" output?
- restart PMF: grow phase required? "lambdaRef"? more documentation on NAMD PMF?
- Restart Simulation
- restart_minimization
- restartfreq question....
- restarting a simulation
- Restarting a Simulation & Langevin
- restarting ABF simulation
- restarting an AMBER simulation (truncated octahedron PBC) in NAMD fails
- restarting calc giving new temperatures
- Restarting calculation missmatches
- restarting files converge to new temperature
- restarting heating protocol problem:
- restarting issue
- Restarting simulation goes the different temperature
- restraining backbone atoms
- restraining parts of a molecule
- restraint on a group of atoms at their center of mass?
- Restraint Potential
- Restraints and System COM Drift
- returning the host list where NAMD runs from an LSF batch system
- reversing constant velocity SMD
- Re£ºHow to fix atoms during minimization?
- right_protocal
- Rigid body effect, translational kinetic momentum
- rigid body model
- Rigid bonds and hydrogen bonds "on" inaccurate/invalid?
- Rise in Total Energy in NVE
- rms gradient
- rmsd calculation for RNA
- rmsd_fullthrotle script problem
- rmsd_RNA_DNA
- RNA_minimization
- Run NAMD in loops
- Run NPT ensemble simulation with sphericalBC?
- Running CGMD using NAMD
- Running Error: The periodicity of dihedral #2 is zero
- Running minimization, heating and FEP simulation within the same configuration file.
- Running Multiple TMD simultaneously
- Running NAMD at TACC (Ranger)
- running namd on cluster
- Running NAMD on Cluster machine with Myrinet network with MPI and PBS
- running namd with condor
- running NAMD with ranger@tacc
- Running NVT simulations
- running precompiled NAMD with multiple processors
- Running thermal unfolding with nose hoover langevin piston
- running_NAMD_on_ALPHA_workstation
- Rv: Value 99999999.9999 during minimization
- S-OXY CYSTEINE parameter
- SAMs using NAMD
- saving the coordinates for huge trajectory file
- Say "NO" to erectile dysfunction!
- scalability problem on linux cluster
- Scalability problem with NAMD2.6 on Intel Xeon EM64T processors
- scaling issues in distributed environment
- scaling the interaction energy
- Scaling the Tiny benchmark
- scripting in namd
- Scripting: Handle for energy terms in the PSF file?
- Seeking suggestions to decide on realistic configuration values
- segmentation fault when running ABF
- segmentation fault when running ABF]
- segmentation fault: Please Help
- segmentation fault?
- Segmentation violation when running without an internet connection
- seperate files-par, top and pdb files for solvents, needed?
- serine phosphorylation modeling
- setting solvent density during solvation
- Sexual power
- SGE and NAMD
- SHAKE: Constrain EVERY bond length and bond angle
- Shear flow: Lees-Edwards Boundary Conditions
- SIDECHAIN _RMSD
- SIDECHAIN _RMSD_Thank_you
- Simple query
- Simple TCL (Forces) question - defining bond vector
- Simulated annealing out of mainstream
- Simulating air with NAMD
- Simulation explodes as soon as minimization starts "GRADIENT TOLERANCE: nan"
- Simulation in water sphere meet with a FATAL ERROR about Bad global exclusion count
- Simulation issues: water box deformation after minimization and shifting protein coordinates during production run
- Simulation of Eukaryotic membrane protein
- simulation of fullerenes
- Simulation of large bilayer crashes with "ERROR: Stray PME grid charges detected"
- Simulation of Thiolated Biotin-Streptavidin on Gold
- simulation problems
- Simulation stalled at startup
- Simulation with non-periodic boundary condition
- simulation_of_big_membrane
- Simulations with large number of constraints crash at startup phase 1 on Indiana's Bigred
- Single topology FEP
- size of water box
- SMD and CPT?
- SMD and CPT? (fwd)
- SMD atoms are not moving in accordance with steering parameters!
- SMD behavior
- SMD Constant Velocity: Force
- SMD ensemble?
- SMD force units
- SMD forces
- SMD in water
- SMD more than once
- SMD of proteins in water box without PBC
- SMD question
- SMD vs RAMD
- SMD vs RAMD / TMD
- SMD-Applied Forces and Analysis
- Soft core potential - tested or not?
- solvate a molecule
- solvate replicates water box (2 by 2 by 2) and segments (8X) for no apparent reason
- solvate using Helmut Grubmuller's SOLVATE and then VMD, then how to minimize properly!
- solvating long protein
- solvating protein
- Solvating protein with ions
- Some question about Target MD
- spawn_namd_command How to properly execute this command
- SPC/E water model
- Specified Electric Field
- spermine force field
- spherical boundary conditions
- srand in a tclforces script
- Stationary temperature gradient - defining 2 langevinFiles?
- steepest descent technique
- steered md with a constant velocity pulling
- Steered MD with NAMD?
- Storage of large files
- Storing atom coordinates at each time step
- storing velocity data of a NVE simulation
- Straining yourself when you are with a woman?
- Strange Input Error
- Strange termination-possible load ballancing issues
- Stray PME grid charges detected
- STRIDE Algorithm
- Struggling with the compilation of NAMD 2.6 on a PBS Cluster with LAM/MPI
- Stupid question about compiling NAMD with cygwin on windows
- submit namd job in cluster
- subscribe namd-l
- Sudden expansion of box when continuing NPT simulation
- sugar topology files
- Sulphate Ion Parameters
- Sulphate Ion Parameters (fwd)
- surface tension
- swig wrapping c++ code on nersc
- Switch ON your penis!
- Switching Function
- Switching PSF files during a run.
- System charge
- system density
- SYSTEM ENERGY MINIMIZATION
- tabulated potentials?
- TARGETED MD - GRADUAL INCREASE OF FORCE
- TARGETED MD ERROR
- Tcl "loadtotalforces" question (forces never seem to be saved)
- Tcl callback, run, revert, measure
- TCL force
- TCL forces
- TCL Forces : OUT OF MEMORY
- tcl forces help
- tcl forces/membranes
- Tcl in NAMD (math::interpolate)
- tcl script for applying constraints
- TCL script for umbrella sampling
- Tcl Scripting
- Tcl-forces query
- TCL/NAMD: FATAL ERROR: error reading output from command: interrupted system call
- TCL8.5? or
- Tcl: callback, run, revert, measure
- TCL: force not a vector
- Tcl_BC: [nexatom] twice in script
- TclBC - multiple iteration
- tclbc example scripts
- tclforce script in FEP: global variable
- TclForces
- TclForces and wrapping
- tclforces: force not a vector
- tclForces: relation between force and velocity
- tclforces: switch from md with external forces to standard md
- 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 rescaling and reassignment parameters
- temperature stepping during heating
- Tests not running for Charm++ Myrinet with MPICH-MX
- Thank you for your advices
- 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 correct topology/parameter file and pgn
- The correlation of SMD force vs. AFM data
- The experimental data of POPE?
- The NAMD job do not go forward
- the relationship between system size and cpu numbers
- the size of membrane?
- Thermodynamic Integration (free energy of conformation change)
- Third node stops the simulation
- Time factor
- Time Step is Incompatible in the NAMD DCD Analyzed with CHARMM
- Time step is incompatible in the NAMD DCD file analyzed with CHARMM
- Timestep
- timestep in TMD
- TIP4 water model NAMD
- tip4p - namd follwup
- TIP4P examples
- TIP4P in NAMD?
- Tired of your poor health?
- TMD
- TMD + harmonic restraints
- TMD + temperature/pressure coupling
- TMD AND RIGIDBONDS
- TMD and RMSD constrained dynamcs
- TMD and TclForces
- TMD bug correction???
- TMD constrained energy
- TMD in NAMD: cannot reach target
- TMD SCRIPT
- TMD SIMULATION - RMSD DOUBT
- TMD: different behaviour between serial and mpi versions
- TMPyP4 force field parameters
- To buy or not to buy?
- To channel bond or not ?
- to heat up the system
- To incorporate an energy term
- too large an area/lipid in POPE bilayers using membrane plugin
- top_all22_model.inp
- top_all27_prot_na.inp and par_all27_prot_na.inp
- Topology cartoon of proteins
- topology file
- topology file for 2 sugar rings connected 1-1 between them
- Topology info - RESidue information for carbon nanotube
- topology of carbon dioxide compatible with Charmm
- topology problem!
- topology/parameter entries for asphaltenes?
- topology/parameter entries for methane?
- topology/parameter file for ligands
- torsion potentials for phi/psi angles in CHARMM force field?
- TOTAL energy increase
- Total external work calculation in SMD-PMF calculation
- total force on atom
- TOTAL, TOTAL2 and TOTAL3
- tracing not available with CMK_OPTIMIZE
- tracing not available with CMK_OPTIMIZE!
- trajectories
- Trajectory file formats & structural alignment
- Translation to NAMD psf file.
- transmembrane electrical potential gradient in NAMD
- Treatment of a Neutral N-terminus
- trifluoroethanol (TFE) solvent
- Trouble in energy minimization with warning to increase cutoff
- Trouble with params file when trying to perform basic dynamics with alanine.
- Troubles with Free Energy of Conformation Change
- Truncated Octahedron for VMD and NAMD simulation
- Turn off H-bonding on select residues
- turn off intermolecular interaction
- Turning off tcl forces
- Two NICs on each node?
- Two questions about free dynamics simulation
- TXT program editor
- Typical maximization steps
- UAB BlueGene
- ubuntu reads my psf as an audio file
- Umbrella Sampling for NAMD
- umbrella sampling of decalanine using the ABF module
- Unable to edit files in NAMD folder.
- UNC Paths in the configuration parameters
- uncharged ends
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- Unfolding protocol..
- Unfolding simulations
- Unit cell angles information
- units of OutputMomenta
- unknown residue LIP
- unsubscribe
- unsubscribe namd-l
- unsubscribe vmd-l
- unsubscribe-namd
- Unsure about current setting of Periodic Boundary Conditions
- unwanted bonds in .pdb file while using molefacture
- use of 'measure hbonds'
- use of charmm27 & NPT ensemble for lipid bilayer simulation
- Use tclforces to find systematic forces on fixed atoms?
- useGroupPressure with no RigidBonds ?
- user defined L-J parameters
- User defined potentials of Lennard-Jones type possible?
- user defined restraint in ABF
- uses of patches for changing the protonation states of residues
- using Amber paramter
- Using CHARMM27
- Using CHARMM27]
- Using NAMD DCD in CHARMM
- Using NAMD to calculate pair energy with many subset permutations
- Value 99999999.9999 during minimization
- van der walls-understanding problem
- Vanishing bonds in small molecule during psf generation.
- variation between results on different OSes
- Varying Force Simulations
- vdW parameter
- vdW parameter for atom type CN7 in ATP
- Vega ZZ Script for calculating area/lipid.
- velocities
- Velocities of different Atoms
- velocity DCD data retrieval
- Velocity scaling and thermostatting both at a time
- Velocity Units
- velocity units in .vel file
- Very peculiar problem while using bigdcd. Help !
- viarecv.c rhandle->len' failed. on infiniband
- virtual and heavy hydrogens in NAMD
- Vlad has Tagged you! :)
- vmd-l:
- vmd-l: C NH1 C minimization error
- vmd-l: CG bead definition
- vmd-l: counting gas molecules inside the nanotube
- vmd-l: DCD for windows
- vmd-l: DNA and low pH
- vmd-l: Fast routines for distance evaluations using PBC.
- vmd-l: Fwd: memory overflow problem of Tcl scripting when dealing with trajectories(sorry for cross mailing...)
- vmd-l: How to calculate the C alpha RMSD from NAMD trajectory
- vmd-l: How to generate more segments?
- vmd-l: How to read specific DCD frames directly in Fortran?
- vmd-l: ionize (big, big, big system!)
- vmd-l: Loading .vel file in VMD
- vmd-l: merging two pdb files
- vmd-l: Small molecules
- vmd-l: TAB key in vmd terminal
- vmd-l: too large an area/lipid in POPE bilayers using membrane plugin
- vmd-l: TXT program editor
- VMD-NAMD-commands
- VMD/psfgen scripting: undefined variable
- VMD/psfgen scripting: undefined variable]
- Want to be a hero in bed?
- Want to be on the top all night long?
- warning about pairlistdist:
- Warning in log file
- Warning: overloaded due to high background load
- water and air box by VMD
- water box getting deformed
- Water density is not 1.0g/cm3
- water HOH angle of 102 defrees
- water models supported in NAMD
- water models: a basic question
- water molecules and silicon wall
- Water molecules inside protein?
- Waterbox unexpectedly deformed after minimization.
- WCA Particle
- Wet miracle
- What does "cellOrigin" really mean?
- 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 is the unit of coupling coefficient when using tCouple to control temperatue?
- which charm
- Which conformation is more proper for the SMD
- Which namd on amd64?
- 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 there is a bond between the two Hydrogens of the TIP3P water in Amber force field?
- Why turning on 'pressureProfile' make NAMD get into sleep?
- Will reducing the cell basis vector in X and Y force my lipids to pack
- won't launch on linux ubuntu cluster for a parallel run
- working with non-protein files
- Worry about your erection?
- Wrap ions?
- wrapping
- Writing to DCD file error - pelase help
- wrong velocity in steered molecular dynamics
- xsc file format
- Your dick is not only for pissing
- Your Pharm4cy 0rder #3728660
- zCoord-1atom
- zCoord-1atom and ** General remark: Subject lines **
- ZINC parameter
- Zinc-NAMD parameters
- Zn parameters
- ´ð¸´: How to build the psf file and the parameter file of a ligand
Last message date: Wed Dec 31 2008 - 05:25:21 CST
Archived on: Wed Feb 29 2012 - 15:48:54 CST
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