NAMD-L: By Subject
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About this archive
Starting: Mon Jan 01 2018 - 09:14:56 CST
Ending: Mon Dec 30 2019 - 20:12:28 CST
- " the error of hydrogen group size "
- "'Hands-on" Workshop on Computational Biophysics at Pittsburgh, PA, May 21-25, 2018
- "-nan" free energy from WHAM analysis
- "block" module for NAMD
- "Child killed: segmentation violation" error when running QM/MM minimization in QwikMD
- "constraint failure in rattle algorithm"
- "Hands-on" Workshop on Enhanced Sampling and Free-Energy Calculation at Urbana, IL, September 10-14, 2018
- "Hands-On" Workshop on QM/MM Simulations at Urbana, IL, April 5-7, 2018
- "non-numeric floating-point value" error while using distanceXY
- "the error of movement of atoms"
- (no subject)
- 1-D ABF and Compressibility
- =20=20none?= quilibrium SMD with fixed atoms
- [ REST2 ] Possible bug on NAMD example
- [External] running NAMD with Slurm
- [External] running NAMD with Slurm on cluster
- [NAMD] Apply an electric field only in a specific region
- [NAMD] Define time-dependent grid force
- [namd] Help with sortreplicas
- [NAMD] How to decompose REUS results into electrostatic and van der Waals contributions
- [NAMD] Running REUS in many nodes
- [NAMD] Units of Efieldfreq
- [VMD-NAMD] Question about Dipole of DNA / Dipole Moment Watcher Plugin
- ABF and Kinetic Barriers
- ABF Asymmetry
- ABF Question
- ABF Questions
- ABF simulations with singularities?
- ABF Window Boundaries
- ABF, rigid bonds and constraints
- About changing charge/multiplicity during QM-MM
- About CUDA version
- About restarting QM-MM simulation
- Accelerated MD with transmembrane protein
- accelMDbdihe is not working properly in NAMD after commit e3e849639982dcba9a60c6072c81fdb7cba69759
- accelMDdihe is not working properly in NAMD after commit e3e849639982dcba9a60c6072c81fdb7cba69759
- Acceptable Timescale fro NAMD
- accepter
- acceptor
- adaptive biasing force
- Adding H-bonds to neutralize GNR built using Nanotube Builder in VMD
- Affinity
- Alchdecouple for dihedral/improper terms
- Alchemify?
- alculate energy force field
- all-atom to coarse-grained system
- AMBER force field parameters
- AMBER NetCDF file for Simulation
- Amber topology for mutation
- Angle list
- Angle of lone pair in TIP4P 2005 simulation
- Any NAMD-Working Small Organic Molecule
- Are there plans on thermostat groups?
- Aromatic rings don't maintain the planarity during the heating
- At high cutoff: "ERROR: CALCULATED VDWA FORCE MAY NOT MATCH ENERGY! POSSIBLE BUG!"
- atom moving fast error in Coarse grained simulation: even reduced the time step
- Atom velocity error in coarse grained simulation using MARTINI
- Attachments allowed?
- auto psf file generation
- AutoPSF charge generation
- AutoPSF Error
- Average structure using colvars
- AW: Are there plans on thermostat groups?
- AW: Aromatic rings don't maintain the planarity during the heating
- AW: AW: AW: Periodic cell has become too small for original patch grid
- AW: AW: How to run a TCL proc at every step in NAMD using callback command?
- AW: AW: Periodic cell has become too small for original patch grid
- AW: Bad structure after converting the coarse grained last frame to all-atom
- AW: Difference between REMD replica temperature and actual temperature
- AW: does any body know why GPU Acceleration not work on Windows?
- AW: How to run a TCL proc at every step in NAMD using callback command?
- AW: Hydrogen Mass Repartitioning in NAMD
- AW: Large number of simulations in parallel using replica exchange.
- AW: Low global CUDA exclusion count! (9592 vs 9618)
- AW: mpi with NAMD
- AW: MSM grid values
- AW: NAMD SMP version warning - Reg
- AW: NAMD with infinite cutoffs?
- AW: patch for cystein bond
- AW: Periodic cell has become too small for original patch grid
- AW: restarting Gaussian accelerated MD fails
- AW: slow down when running 2 simulations on 1 node
- AW: strange benchmark results -- how would you explain them and what would you advice?
- AW: Velocity unit
- AW: Weird PBC wrapping
- Bad global bond count! (48842 vs 48843)
- Bad structure after converting the coarse grained last frame to all-atom
- Barostat dimension rescaling under semi-isotropic pressure coupling conditions
- Best water model
- Better way to fix the atom -Reg
- Big oscillations during QM/MM minimization
- Binding free energy tutorial
- Bond parameter error for the system which has been converted using residue-based coarse-grained method
- bpti example compiled source charmrun++ does not launch
- Broken Structure after reverting coarse-grained system to all-atom system
- Bug in NAMD
- Bug in NAMD (was: Big oscillations during QM/MM minimization)
- Bug with FEP?
- BUG: ReplicaUniformPatchGrids and "output" command namd-2.13NB
- BUG? reinitatoms on wrapped coordinates occasionally fail with rigidbonds
- Bugs and Questions
- Build for CUDA support
- Building of NAMD on the Linux cluster with InfiniBand
- Building with GCC on Ubuntu 18
- C36 force field
- Calculate energy of a residue using NAMD energy
- Calculating hydrophilic and hydrophobic Solvent Accessible Surface Area
- Calculating Interaction Energies Using NAMD Energy Plugin
- calculating non bonded energy using namdenergy
- Calculation of Diffusion coefficient
- calculation of helical axis in NAMD
- Can't set multiple harmonic restrains in colvar module
- catalysis mechnism of ATPase
- CG simulation of water molecules -Reg
- CGenFF 4.1 lone pairs
- changing value of coulomb constant
- CHARMM FF parameters for FE-S bond in CYP450
- CHARMM force field for Hydrogen bond?
- CHARMM36 parameters for nucelobases
- charmrun error: Work completion error in sendCq
- Cleaving and capping protein with autopsf leads to parameter errors upon running NAMD
- CMIAbort Error
- Coarse Grained simulation of silicon nitride nanopore - Reg
- Coarse-grained umbrella sampling for POPS-protein system
- Colvar not working in NAMD2.12 Linux version
- Colvar orientation of polymer
- colvar restraint simulation
- colvar setting, targetcenters not working
- colvar with moving frame of reference
- Colvars alternative recommendations
- Colvars and distance restraint for umbrella sampling
- Colvars Orientation Question
- Colvars Restraint Question
- colvars selecting frames
- Colvars: Are the derivatives of optimal rotation matrix wrt atomic coordinates applied implicitly?
- colvars: How to implement a collective variable of vector type?
- Colvars: implement a CV which requires computing minimal RMSDs with respect to multiple different reference frames
- colvars: make an extended CV periodic
- colvars: Questions about the metadynamics hillWIdth option.
- COMmotion -- is it a good practice to turn it on for a restart?
- Compiler and version used by jenkins to test patch sets
- Compiler segfault when building 2.13 with GCC 8.x
- compiling infiniband version of NAMD
- compiling NAMD 2.13 make error
- Computational electrophysiology
- Concatenate Outputs
- Constant Force Pull
- Constant Force SMD Question
- constant temprature for vacuum condition in namd file
- Constant Velocity Pulls
- Constant Velocity SMD Question
- Constraint failure in Highly charged system - Reg
- Constraint failure in rattle algorithm for some atoms, simulation becomes unstable
- constraint-force constant
- Consulting about buying new hardware (GPU)
- Continuing metadynamics run
- convert a 3d system into a 2d system
- Converting a mixture system from NAMD to LAMMPS
- Converting GromacsForce File to NAMD using GromacsTopFile.C
- Couldn't open DCD file
- Creating an infinite graphene sheet
- creating topology for a unique structure
- Critical isofrom selectivity in molecular dynamics
- CSVR + eABF, system temperature set to zero
- Cuda
- CUDA acceleration on Windows 10 doesn't work
- Cutoff radius for electrostatic embedding in QM/MM calculations
- CZAR Estimator: grad file
- Decreasing performance of cluster running FEP
- detecting vanishing atoms in zero.fep
- Didn't Find vdw parameter QMMM
- Dielectric Constant in the gas phase
- Difference between REMD replica temperature and actual temperature
- Differences between z-gradient and gradient in ABF simulation
- Different cell vectors - Reg
- Different resid in pdb fie but showing same molecule in VMD
- Diffusion Coefficient calculation
- distance filter during data analysis
- Distance restraints
- Distorted peptide bond with new residue
- Distortion in Structure Minimization
- DNA won't translocate through graphene nanopore
- Do firsttimestep, numsteps and run have maximum values?
- does any body know why GPU Acceleration not work on Windows?
- Does umbrella sampling need same sampling steps for each windows?
- Double-defined segid, resid for more than 9999 id's
- Doubt about ABF and PMF file generation
- Doubt in generating Ficoll 70 Hard Sphere for Coarse Grain Simulation
- Dual topology FEP for anions
- Dual Topology in FEP Calculations - How to Calculate Electrostatics and van der Waals Free Energies Separately?
- dummyAtom in distance colvar in ABF calculations
- E-field to Voltage - Reg
- E-filed to individual channel in parallel system - Reg
- effect of acceptors
- electric field- forces in NAMD source code
- Electrostatic interaction of 2 ions
- Enabling charmrun in NAMD simulation
- energy calculation with namdenergy
- Energy Minimization failure for mutants
- Energy Minimization Simulation
- Enhanced Sampling and Free-Energy Calculations Lectures
- enhanced sampling of flexible tail
- Enthalpy Question
- EPW "ATOMS Moving too fast"
- Equilibrated TIP4P_2005 Waterbox
- Equilibration in NPT simulation
- Equilibration of membrane water system (pressure in NVT)
- ERROR During MPI run
- Error during simulation
- error in (runfepmin)
- error in compiling namd
- ERROR in multiple walker metadynamics simulation
- Error in NAMD Simulations -Drude
- Error in PMF Calculations
- Error in running NAMD on a cluster
- Error in the collective variables
- Error in the Continuation TMD simulation Run.
- Error in the NAMD Tutorial
- Error in using the QMElecEmbed keyword
- Error NPT simulation - Need Urgent Help - Reg
- Error Regarding minimization
- Error running deinterleave_idws.py on FEP simulation output
- ERROR TOLERANCE
- Error while equilibrating AGNR nanopore + DNA system
- Error while runing simulation for protein docking
- Error with D-amino acids mid-sequence using NAMD 2.12/2.13b2 and CHARMm36
- ERROR: Constraint failure in RATTLE algorithm for atom 232! ERROR: Constraint failure; simulation has become unstable.
- Ewald size-dependence correction in FEP simulation of an electric dipole
- Extracting velocities from veldcd file
- FAD topology and parameters
- Fastest way to get PSF file for pure QM simulation?
- fatal error regarding parameters
- FATAL ERROR with "File exists"
- FATAL ERROR: CUDA error CudaComputeNonbonded::forceDoneCheck polled 1000000 times over 154.549621 s on Pe 4 (c36.chundoong device 0 pci 0:2:0)
- FATAL ERROR: Error in QM-MM bond assignment; bonded QM atoms with occupancy=1
- FATAL ERROR: FOUND ISOLATED LONE PAIR
- FATAL ERROR: High global CUDA exclusion count!
- FATAL ERROR: Must have either an initial temperature or a velocity file
- FATAL ERROR: PBC
- FATAL ERROR: Periodic cell has become too small for original patch grid!
- FATAL ERROR: Unable to access config file temp14.conf
- FATAL ERROR: UNABLE TO FIND BOND PARAMETERS FOR CG2O4 CG311 (ATOMS 1220 1222)
- Fatty Acid Topology
- FEP & node/core number
- FEP atom velocity.
- FEP minimum requirements
- FEP performance
- FEP protein-ligand tutorial 2017 unclear section
- FEP Rattle Error
- FEP slowdown
- FEP slowdown during execution
- FEP with intermediary segments
- FEP/REMD (ERROR: 'alchLambda' is a required configuration option)
- ffTK torsion scan convergence using Gaussian.
- FFtK Tutorial (Urey-Bradley angles error).
- ffTK Without Using Gaussian
- First "Hands-On" Workshop on Structural DNA Nanotechnology
- Fix aminoacids - error
- flexible fitting for helical structure
- Force constant for Umbrella sampling and WHAM
- Free energy plot
- Functionality of wrapWater and wrapAll commands for periodic simulations
- FW (1): 71i
- Fwd: About changing charge/multiplicity during QM-MM
- Fwd: Colvars Orientation Question
- Fwd: FEP & node/core number
- Fwd: FEP protein-ligand tutorial 2017 unclear section
- Fwd: FEP slowdown during execution
- Fwd: FEP with intermediary segments
- Fwd: Gromacs to Charmm FF Format Conversion -Reg
- Fwd: Is QM/MM compatible with Colvars?
- Fwd: Ligand atoms moving too fast with FEP
- Fwd: namd on AWS
- Fwd: parameter request for PRES bonding
- Fwd: parseFEP domain error
- Fwd: ParseFEP for restating FEP
- Fwd: pressure in interfacial tension
- Fwd: QM-MM NAMD-ORCA broken symmetry
- Fwd: Question on restraints with MM-GBSA
- Fwd: Running NAMD on Linux Cluster
- Fwd: running NAMD with AMBER inputs
- Fwd: Running QM-MM tutorial on a cluster
- Fwd: Sudden /\A drop in last FEP window
- Fwd: the fep error in third part of config file
- Fwd: Tuning QM-MM with namd-orca on one cluster node
- g++ 5.3 fails on 2.12/2.13b1 with CUDA 8.0
- GaMD in NAMD
- gamd restart file in namd 2.13
- gaussian aMD with iE=2 (setting E threshold at maximum)
- Gaussian Dihedral Scan Log files visualization.
- GBIS parameters
- Get NAMD version from the tcl script interface
- Getting the topology,PSF files
- git rid of it
- GLA (γ-carboxyglutamic acid) topology for CHARMM36
- GolP-CHARMM
- Gradual minimization
- Graphene psf file
- Gromacs to Charmm FF Format Conversion -Reg
- H2 Topology and Parameter files
- Hamiltonian Replica exchange configuration file
- Hamiltonian Replica Exchange MD in NAMD
- Handling of nonbonded lists in PSF - please clarify
- Hard wall on Z direction for ions
- Harmonic restrains
- having problem with disulfide bond
- Having problem with restarting colvar distance,
- hbond restraint simulation
- heating
- Heating problem for protein/ligand complex
- Holding molecules on one side of membrane
- Homologous structure as stating flexible fitting model
- How do I add passivated H-atom to ZGNR
- How does NAMD calculate AccumulatedWork when using RMSD colvar?
- How to add a C code to NAMD properly?
- How to create multiple molecules using psfgen
- How to extend an ABF simulation ?
- How to integrate multiple walkers 2D metadynamics results?
- How to interpret Thermodynamic Integration output
- how to make a .Dx file trajectory to showing the Electrostatic Maps or ion concentration video?
- How to make water stay in the Z direction?
- How to run a TCL proc at every step in NAMD using callback command?
- How to set up a window distance of 2 angstroms in Umbrella sampling
- How to simulate flexible water with TIP4P potential?
- How to solve the segmentation faults in compiling NAMD to build and test the Charm++/Converse library (MPI version)?
- how to switch off hydrogen bonds in TIP4P/2005 water
- how to translate a protein without unfolding
- Hybrid AA/CG for a transmembrane protein system
- Hydrogen mass repartitioning and 4-fs time steps in NAMD
- Hydrogen Mass Repartitioning in NAMD
- Hydronium parameters
- Immediate postdoc opening in Bio-molecular simulation, University of Alberta, Canada
- Included Topology (.itp) in gromacs to parameter file for NAMD
- Induced Electric filed and Electrostatics - Reg
- info about gpu hardware
- Info on solutescaling
- inputPrefix merge error ABF
- Ion concentration and aggregation problem of the nuclear protein simulations
- Is QM/MM compatible with Colvars?
- Is there a problem of ORCA running for NAMD MPI?
- Is there really no way of automating pair interaction calculations without invoking NAMD for each pdb file separately?
- Is there someway to render protein picture without background color?
- Isomerization between runs
- Issue using qwikMD with an uncommon cofactor
- Issue With CatDCD in Dynamical Network Tutorial
- Job submission error for NAMD-2.13 ( version netlrts with cuda-10.0) using Torque job scheduler
- Jobs and Evens in CHARMM-GUI
- Langevin Dynamics Coefficient Value -Reg
- Large number of simulations in parallel using replica exchange.
- Lennard-Jones Potential
- Ligand atoms moving too fast with FEP
- Lipid bilayer deformed during coarse grain simulation
- long simulation and error "integer value too large"
- looping on multiple dcds in namd configuration file
- Low global CUDA exclusion count! (9592 vs 9618)
- Lowe-Andersen Thermostat Speed
- Machinefile Question
- Magnetic field
- mail about autoionize plugin
- mail about constraints in namd configuration file
- mail about error in configuration files
- mail about error in namd compilation
- Mail about force field parameters
- MAIL ABOUT INTRODUCING NEW residue
- MAIL about namd velocity error
- mail about non bonded parameters
- mail about pbs script
- mail about tcl script
- mail about usage of water tcl script in membrane
- Mail from vidhyasankar
- mail reg constraint force
- mail reg Namd compilation
- MAIL REG NAMD PBS SCRIPT on mpi cluster
- Mailing list for Postdoctoral opportunities in Simulations
- Make error in compiling NAMD source code
- making new psf file from .prm and pdb file
- MAOL ABOUT USAGE OF TCL SCRIPT
- Martini CG parameter errors for lipids
- Maximum Timestep for NAMD
- MD Simulations with GROMACS/NAMD/AMBER/VMD: Seasonal School in Stockholm 10-13 June
- MD without water - Reg
- mdff for EM map with helical symmetry and the asymmetric unit is dimer
- Meaning of warning in output log file
- Membrane Simulation
- Merge File Question
- merging abf trajectories with different number of colvars
- metadynamics problem
- metadynamics reaction coordinate
- Microtubule Simulation
- minimization
- Minimization Error
- Minimization Question
- Mismatch in atom number between psf and dcd files
- Missing cphrst file
- Missing Parameters For H3O+
- mistakes in the user guide in the accelerated MD section ?
- Modifying LJ Potential -Reg
- MOPAC Plugin Update
- MOPAC Point Charges
- mpi with NAMD
- mpirun was unable to find the specified executable file
- mscs.pdb
- MSM grid values
- Multi canonical ensemble method
- Multi-dimensional PMF
- Multi-node job errors
- multi-node mpiexec issue
- Multiple Colvars
- Multiple Constraints Equilibration
- multiplot: Data vector empty, ignoring plot!
- Namd
- NAMD 2.12 Volta Compatibility
- NAMD 2.13 and RTX2080Ti
- NAMD compiling problem
- NAMD configuration file
- NAMD Configuration file error
- NAMD Developer Meeting 2019
- NAMD Developer Workshop at Urbana IL, June 11-12, 2018
- NAMD Error
- NAMD hangs at "Load balancer assumes all CPUs are same." when runs on an infiniband cluster.
- namd mpi
- namd on AWS
- NAMD on Windows 10 with huge performance drop after 39 CPUs
- NAMD QM/MM alchemical free energy change capabilities?
- NAMD run on Intel hyperthreaded cores
- NAMD Simulation in a laptop
- namd simulation input file setting from NPT to NVT
- NAMD SMP version warning - Reg
- NAMD support for lone pairs
- NAMD with infinite cutoffs?
- NAMD+PLUMED
- NAMD-CUDA GPU workload
- NAMD-QM/MM TUTORIAL: Atoms moving too fast error
- NAMD/VMD installation for Windows 10
- namd2 GPU error
- namd2_ti.pl Error: Modification of non-creatable array value attempted
- namdstats.tcl problem
- nan (Not a number) error in meta-eABF simulation
- Nano-bio interaction in NAMD
- need help in study the effect of mutation,
- Need help preventing hydration of the lipid-protein interface
- Need help preventing hydration of the lipid-protein using tcl script
- Need help with errors in REST2 sample file
- Need help with psfgen : psfgen can't read file.pdb
- Negative step number
- New version of Molefacture -small molecule modeling tool- posted
- Non bonding energy calculation through NAMD
- non uniform attempts distribution in constant pH MD
- nonequilibrium SMD with fixed atoms
- nonuniform sampling in ABF
- Number of QM Atoms Error
- NVIDIA Quadro(R) GV100 card for NAMD studies
- OPC Water Model
- ORCA GPUs
- ORCA NAMD Parallel
- ORCA Orbital Bug
- ORCA QMMM
- orca_plot asking .xyz file from QM-MM
- Orientation Colvars Question
- overlapping windows in ABF
- Pair interaction energies: TCL error -reg
- pairlist question
- Parallel Jobs
- Parallel Simulation Question
- parameter
- Parameter and Topology File Question
- parameter file for ACE and CT3 cap
- Parameter Optimization Advice
- parameter request for PRES bonding
- parameters and topology for Deacylcortivazol (DAC)
- ParseFEP error
- ParseFEP error with FEP in segments at different lambda schedule
- ParseFEP for restating FEP
- patch for cystein bond
- patch for threonine (THP2).
- patch ID error
- PBC and restraints
- PBC error. Amber force field in NAMD
- PCA and vector
- PCA calculations
- PDB structures of peptides
- Performance on GPU
- Periodic boundary condition
- Periodic cell basis too small for GridForce
- Periodic cell has become too small for original patch grid
- Ph.D. and Post-doc positions in molecular simulations and structural bioinformatics
- Ph.D. candidate position in biomolecular modeling or bioinformatics
- Phosphorylated Residues
- Phosphotyrosine Parameters/Toplogy
- PME Tolerance
- PME with Implicit solvent - Reg
- PMF calculation
- PMF calculation using CPU and GPU
- Pointcharge file in QM/MM setup with ORCA
- position restraint only certain residues during minimization
- Positive energy for protein
- Positive energy values for protein
- Positive VDW energies
- Postdoc Position at Penn in Chromosome Modeling
- Postdoctoral researcher position in computational virology.
- pre compiled charmm-6.8.2 for namd2.13 nightly version compilation for multiple GPU node simulations
- pre compiled namd2.13 version nightly build for Linux-x86_64-verbs-smp-CUDA or help with compiling charm++
- Pressure ? High values ; Pressavg Gpressavg ? value of first step of restart very different from the last of the previous MD
- Prevent DNA denaturation
- Problem generating pdb psf of ATP
- Problem in generating psf
- Problem in NAMD memory optimized version - Reg
- Problem in Running CUDA-Enabled NAMD Via MOE software
- Problem with compiling vmd from source code
- problem with minimizer
- Problem with namd 2.13 constant pH molecular dynamics, HSD residue.
- problem with solvating a structure
- Problems about constraint (conskcol) in umbrella sampling conf file
- problems running GPU-accelerated namd
- Problems with temperature control.
- Proper use of psfgen "mutate"?
- Protein Charge
- Protein Deformity in Implicit Solvent Simulation
- protein movement
- Protein:ligand standard binding free energies
- psf from parmed
- PSFGEN 1.6.4 autogenerate PATCH keyword not available
- psfgen error protein-ligand
- Pulling only one half of a harmonic restraint
- Python based tool for analysis of DCD trajectories
- Python Wrapper Bug
- QM-MM and transition elements
- QM-MM NAMD-ORCA broken symmetry
- QM-MM with MOPAC
- QM/MM Error
- QM/MM error: The number of QM atoms received is different than expected
- QM/MM internal energies
- QM/MM MD and the qmParamPDB file
- QM/MM Question
- QM/MM with Orca: Memory allocation failed
- QMMM 1 Node vs Multinode
- QMMM FEP
- QMMM Frequency Calculation
- QMMM ORCA Error
- QMMM Question
- qmSecProc Proper Use
- Query for coarse grain system
- question
- Question about "useConstantArea" in puresure control model
- Question about colvars
- Question about PMF calculation
- question about SMD
- Question about the fundamentals of MD and WHAM
- Question on making 'reversible' solvated simulation
- Question on restraint behavior when part of system decouples
- Question on restraints with MM-GBSA
- question when apply external electric field
- Question: constant-pH to standard MD
- Qwikmd ABF Question
- QwikMD Question
- QwikMD SMD force calculation
- Random Velocities Question
- Rattle algorithm Constraint failure - Reg
- Rattle error with lateral pressure calculations
- RDF of hydroxide ion in a water box
- re-centering the molecule while restarting the run
- readmol2 warning: non-unique atoms were renamed.
- Reduce verbosity during minimization
- Reg autioionize plugin
- Reg membrane hydration
- Reg Membrane simulation
- reg nan error in namd
- Reg: Docking
- Reg: Force Field file
- reg: quenching NAMD trajectory
- Reg: Solvation box
- Regarding FICOLL 70 & PEG20000
- Regarding free energy
- Regarding free energy calculation
- Regarding Hard sphere
- Regarding number of water molecule
- Regarding PCA
- Regarding psf generation
- Regarding Topology and Parameterization
- regarding umbrella sampling simulation
- reinitatoms
- Reload molecular topology for amber files?
- REMD restart tcl script meaning?
- REMD using remote GPU
- Reminder NAMD Developer Meeting 2019
- Replica exchange simulation with GPU Accelaration
- Requesting abstracts for MRS Fall 2018 Symposium BM03: Multiscale Modeling of Soft Materials and Interfaces
- Research Programmer for VMD/NAMD at UIUC
- Research Programmer Positions Available
- Residue Charges
- REST and Periodic Cell Issues
- Restart Annealing
- restarting Gaussian accelerated MD fails
- restrain lateral movement during ABF
- restrict atoms to cross a boundary
- Restrict drift of Graphene sheet in X-Y plane using Colvars
- reverting atoms introduced by name into standard PDB ones
- Reverting coarse-grain system to all-atom system
- Right NAMD version
- rigid body simulation with NAMD
- run different simulation of the same system by using different initial velocities
- run MD simulation in NAMD using stages file strategy or all in one file ?
- run MD simulation in NAMD using stages file strategy or allin one file ?
- Running broken-symmetry with namd-orca
- Running MD simulation for two molecules
- Running multiple walker metadynamics on Stampede2
- Running NAMD in MPI environment
- Running NAMD on Amazon AMI
- Running NAMD on Linux Cluster
- running NAMD with Slurm
- running NAMD with Slurm on cluster
- Running on GPU
- running pair interaction analysis multiple dcds in sequence in single run
- Running QM-MM MOPAC on a cluster
- Running QM-MM multinode
- Running QM-MM tutorial on a cluster
- Salvation of non-orthogonal box
- Same timestep for my simulation run is coming more than once and in random order in the log file
- scriptedColvarForces doesn't work in recent NAMD builds
- Segfault during NAMD compilation with GCC 8.3
- SegFault in QM/MM run
- Segmentation fault
- Segmentation fault for the tutorial
- Selected cofactor in final output
- Selecting waters from dynamics trajectory
- Selective accelerated MD in NAMD
- Sending REUS simulations to Stampede
- Setting alchElecLambdaStart 1.0 parameter for FEP calculations
- Setting up amorphous SiO2 slab
- Setting up GPU workstation advice
- Setting up QM/MM calculations with QwikMD without the GUI
- Several issues (possible bugs) in REST2 - soluteScalingFile & langevinTemp
- Should a pairlist warning concern me?
- Simple PME Question
- Simulating a Binding Event
- simulation becomes unstable in residue base coarse grained system
- Simulation crashes during annealing the reverted all-atom structure
- Simulation of imprinting process in NAMD
- Simulation of sodium dodecyl sulfate
- slow down when running 2 simulations on 1 node
- SM Bargeen A Turzo wants to share the file Min_error with you
- SMD for understanding the proximity of two atoms
- SMD negative forces
- SMD with colvar not working
- SMD: Combined Constant Velocity and Constant Force method
- SMwST RATTLE Algorithm
- solute scaling does not affect electrostatics (and other quirks)
- Solutescaling not working with Amber files
- Solvate with methanol and acetone using free energy methods in NAMD?
- solvating silica
- Some questions about restrained-ensemble molecular dynamics (reMD)
- Spectre/Meltdown patch performance hits
- Standard binding free energy protein-ligand (ABF)
- Standard density -reg
- Standard Error Calcuation
- statistical error in ABF calculations
- Steered MD simulation with pull and rotation
- Stochastic velocity rescaling for Free Energy calculations
- strange benchmark results -- how would you explain them and what would you advice?
- Strange Bond Behavior Question
- Stress calculation
- String Method with Swarms of Trajectories (SMwST) Performance
- Sudden /\A drop in last FEP window
- Sudden drop of /\A in ParseFEP.log near lamda 1.0
- Support of recent Amber force field
- Surface Tension calculation
- Swarms Errors
- SWM4-NDP PSF File
- tar.gz incorrect firmat?
- Targeted molecular dynamics domain selection question
- TCBG Workshop lecture videos
- TCBG Workshop lecture videos😝😚😚
- TclBC forces on individual atoms
- temperature accelerated molecular dynamics
- Temperature Fluctuations in Drude Simulations - NAMD
- TeraChem
- TeraChem QMMM
- the fep error in third part of config file
- the instance type selection for NAMD simulation in Amason marketplace
- Thermodynamic Integration document
- Thermodynamic integration output analysis
- Three bonds with water in vmd from NAMD DCD
- Tilting angle of lipid calculation
- TIP4P water box
- TMD Partial Fitting Problem
- torsion scan
- Total charge problem
- trouble with colvars module
- Trouble with NAMD Win64-CUDA 2.12 on my new PC
- Tuning QM-MM with namd-orca on one cluster node
- Tutorial
- Umbrella Sampling in PLUMED + NAMD
- Umbrella Sampling input parameters
- Umbrella sampling of a protein through a membrane
- UNABLE TO FIND ANGLE PARAMETERS FOR CD OH1 CD (ATOMS 282 284 282)
- UNABLE TO FIND ANGLE PARAMETERS FOR CT OS HO (ATOMS 23662 23661 23656)
- unable to open restart.colvars
- Unexpected Energy values - Reg
- unit dipole moment vector
- Unit of Force constant of position restraint
- Unusual WT-Metadynamics gaussians heights
- Update particle position iteratively in between steps
- use Colvars to track four group of pair atoms distance at same time?
- User force field with FEP?
- Using 4-site water model in NAMD
- Using amberFF and NAMD
- Using center of mass to calculate the radial distribution function
- Using harmonic walls on water molecules
- Using PBC tools for a cubic and a rectangular box
- Using restraint on the dye using radius of gyration value in namd
- Utilising the GPU in NAMD((NVIDIA CUDA acceleration) in windows
- vacuum condition in config file
- vacuum simulation -Reg
- variation of pressure
- veccross implementation in tclforces
- vecsub:two vectors don't have the same size
- Vectors and indexing in VMD
- Velocity unit
- velocity.pdb and velocity unit in NAMD
- Vibration Analysis Script
- vmd-l: [VMD-NAMD] Question about Dipole of DNA / Dipole Moment Watcher Plugin
- vmd-l: Bugs and Questions
- vmd-l: Enhanced Sampling and Free-Energy Calculations Lectures
- vmd-l: Fwd: FEP with intermediary segments
- vmd-l: Fwd: parseFEP domain error
- vmd-l: Fwd: ParseFEP for restating FEP
- vmd-l: Getting the topology,PSF files
- vmd-l: Large number of harmonic distance restraints
- vmd-l: ORCA Orbital Bug
- vmd-l: PDB structures of peptides
- vmd-l: Proper use of psfgen "mutate"?
- vmd-l: PSFGEN 1.6.4 autogenerate PATCH keyword not available
- vmd-l: query on how to allow the protein to interact with the water molecules
- VMD/NMAD on AWS
- water box tilts during equilibration
- Water Molecule Issue
- Water Transport
- Way to wget or curl download the precompiled NAMD?
- Ways to find water molecules passing through the water channel in lipid bilayer
- we apply a harmonic potential
- Weird PBC wrapping
- What NAMD version to obtain
- what's the latest on using NAMD (and MD in general) for docking?
- When using WHAM TO ANALYSIS
- Which one is more reliable to use in umbrella sampling- .traj data or vmd script data
- Which parameters to use in the MD simulation of defected carbon nanotube/graphene?
- Wrapping multimeric protein issues
- Wrong result in running QM/MM simulation with a small test system
- xMDFF: model file is not given
- Zero PME pencils found
Last message date: Mon Dec 30 2019 - 20:12:28 CST
Archived on: Tue Dec 31 2019 - 23:21:06 CST
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