NAMD-L: By Subject
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About this archive
Starting: Tue Jan 01 2019 - 03:25:13 CST
Ending: Thu Dec 31 2020 - 22:29:33 CST
- " the error of hydrogen group size "
- "-nan" free energy from WHAM analysis
- "constraint failure in rattle algorithm"
- "the error of movement of atoms"
- (no subject)
- .coor and .vel output files not generated
- << Conformational sampling with NAMD >>
- << Setting the simulation time parameters >>
- [3.0alpha5] Low global CUDA exclusion count. System is stable without cudaSOAIntegrate or without rigidBonds.
- [External] how i can utilize 4 GPU in simulation with poor performance
- [External] running NAMD with Slurm
- [External] running NAMD with Slurm on cluster
- [NAMD] Example of submission script on Comet/Stampede GPUs
- [namd] Help with sortreplicas
- [NAMD] How to decompose REUS results into electrostatic and van der Waals contributions
- A home PC to run NAMD simulations
- A question about the code in CudaPmeSolverUtilKernel.cu
- ABF and Kinetic Barriers
- ABF Not Sampling Whole Window
- ABF protocol to calculate PMF
- About changing charge/multiplicity during QM-MM
- about geometrical restrain protein on membrane
- About restarting QM-MM simulation
- About the well-tempered metadynamics convergence..
- Accelerated MD with transmembrane protein
- Acceptable Timescale fro NAMD
- acetylene
- actual production MD
- Adding bias potential
- Adding H-bonds to neutralize GNR built using Nanotube Builder in VMD
- adding peptide constraint in NAMD configuration file
- Advice for Protein Mutation FEP Calculations
- Alchemical Transformation for calculation of standard binding free energies
- alculate energy force field
- amber force field
- AMBER force field parameters
- AMBER input and REST2 leads to crash
- Amber topology for mutation
- Amber14 in NAMD 2.13
- Ambiguity among number of residues as counted in VMD and PyMol for RMSF
- Analysis of force applied to a certain atom
- Angle list
- Annealing stepin QwikMD of VMD
- Any NAMD-Working Small Organic Molecule
- Assessing total time of run in NAMD
- Asymmetric concentration gradient: non-periodic z-boundary for only ions
- Atom outside of the MSM grid in NVT simulation - Semiperiodic boundaries
- Attachments allowed?
- auto psf file generation
- AutoPSF charge generation
- Average structure using colvars
- AW: does any body know why GPU Acceleration not work on Windows?
- AW: Hydrogen Mass Repartitioning
- AW: Large number of simulations in parallel using replica exchange.
- AW: mpi with NAMD
- AW: MSM grid values
- AW: NAMD with infinite cutoffs?
- AW: patch for cystein bond
- AW: restarting Gaussian accelerated MD fails
- AW: slow down when running 2 simulations on 1 node
- AW: Slow performance over multi-core processor and CUDA build
- AW: strange benchmark results -- how would you explain them and what would you advice?
- AW: Velocity unit
- AW: vmd-l: How to increase the number of core
- bad angle error!!
- Bad global bond count!
- Barostat dimension rescaling under semi-isotropic pressure coupling conditions
- Basics of MD
- Big oscillations during QM/MM minimization
- Bond between custom ligand and protein sidechain
- Box of Water
- Bug in NAMD
- Bug in NAMD (was: Big oscillations during QM/MM minimization)
- BUG? reinitatoms on wrapped coordinates occasionally fail with rigidbonds
- Bugs and Questions
- Building of NAMD on the Linux cluster with InfiniBand
- Bypassing MM parameterization of ligand in QMMM
- Calculating 2D PMF from 1D eABF simulations using CZAR estimator.
- Calculating Interaction Energies Using NAMD Energy Plugin
- Can NAMD 2.13 be build on Charm++ with UCX backend?
- Can Namd 2.14 and genpsf 2.0 process halogen bonds?
- Can't set multiple harmonic restrains in colvar module
- catalysis mechnism of ATPase
- Cations spontaneous binding pathway with PMF calculation?
- Cavernous Depressions in Water Box
- Centre of mass distance in ABF
- CG simulation of water molecules -Reg
- changing value of coulomb constant
- CHARMM force field for Hydrogen bond?
- Charmm hybrid topology
- CHARMM36 to Drude conversion for NAMD
- charmrun error: Work completion error in sendCq
- Collaboration offer
- Colvar not working in NAMD2.12 Linux version
- Colvar orientation of polymer
- colvar restraint simulation
- colvar setting, targetcenters not working
- COLVARs for Cremer-Pople puckering parameters in NAMD Metadynamics
- Colvars Harmonic Bias Force Direction
- Colvars Orientation Question
- Colvars: Are the derivatives of optimal rotation matrix wrt atomic coordinates applied implicitly?
- Colvars: implement a CV which requires computing minimal RMSDs with respect to multiple different reference frames
- COMmotion -- is it a good practice to turn it on for a restart?
- Comparison of electric field between MD simulation and Experiments
- Compile NAMD on Windows 64 bit; nocuda, multicore
- Compile NAMD with PLUMED
- 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
- Conformation Sampling tutorial: factor of 2 in monitor.sh
- Constant Force SMD Question
- Constant Velocity Pulls
- Constant Velocity SMD Question
- Constraint failure in rattle algorithm for some atoms, simulation becomes unstable
- constraint-force constant
- Convert solvated CHARMM PDB + PSF to Amber
- converting gromacs topology file to namd
- CpHMD: Warning when building atom of unknown mass (psfgen)
- CPU vs GPU Question
- CPU/GPU Distribution
- CSVR + eABF, system temperature set to zero
- Cuboid water box issues
- Cuda
- CUDA acceleration on Windows 10 doesn't work
- CUDA Error
- Dcd file abnormal termination please help
- DCD File Not Generating
- Dcdfreq Variable Value Question
- Degrees of Freedom in REST2
- Didn't Find vdw parameter QMMM
- difference between numsteps and run in step4_equilibration.inp
- Differences between z-gradient and gradient in ABF simulation
- Different Velocity or Margin Errors for Restarted Simulation
- Distance restraints
- Distortion in Structure Minimization
- DNA won't translocate through graphene nanopore
- does any body know why GPU Acceleration not work on Windows?
- Does NAMD have unit tests or how can I confirm the correctness of the simulation results of NAMD?
- Does umbrella sampling need same sampling steps for each windows?
- Doubt about ABF and PMF file generation
- Doubt in generating Ficoll 70 Hard Sphere for Coarse Grain Simulation
- DRMS Colvar
- Drude equilibration
- Drude polarizable force field
- Dual topology FEP for anions
- Dynamic switching GPU/CPU minimization
- Electrostatic interaction of 2 ions
- Energy Minimization Simulation
- Enthalpy Question
- EPW "ATOMS Moving too fast"
- Equilibrated boxes of organic solvents
- Equilibration of a solvated CNT using C36
- ERROR During MPI run
- Error during simulation
- Error generating files with QwikMD
- error in compiling namd
- Error in fftk during bond opt using VMD 1.9.3
- Error in PMF Calculations
- Error in running NAMD on a cluster
- Error in the collective variables
- Error in the NAMD Tutorial
- Error in using the QMElecEmbed keyword
- Error Restarting Simulation
- Error running command for QM forces calculation
- Error running deinterleave_idws.py on FEP simulation output
- Error when using namdplot
- Error while equilibrating AGNR nanopore + DNA system
- Error while runing simulation for protein docking
- error with namd2_ti.pl script
- ERROR: Atoms (still) moving too fast
- ERROR: Atoms moving too fast; simulation has become unstable
- ERROR: Atoms moving too fast; simulation has become unstable (2 atoms on patch 42 pe 18).
- ERROR: Constraint failure in RATTLE algorithm for atom 232! ERROR: Constraint failure; simulation has become unstable.
- error: minimizer slowly moving xxx atoms with bad contacts downhill
- Error: Number of NGauss expected in AddNewGTOs
- Exit code 127 with QMMM
- Extra frame at start of each trajectory
- Extracting velocities from veldcd file
- Farnesylated Cysteine
- Fastest way to get PSF file for pure QM simulation?
- FATAL ERROR in protein minimization by drude model : UNABLE TO FIND ANGLE PARAMETERS FOR CD2O1A OD2C1A LPDO1
- fatal error regarding parameters
- FATAL ERROR with "File exists"
- FATAL ERROR: can't read "boxtype"
- FATAL ERROR: Charge placement error in QM-MM bond.
- 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: EOF ENCOUNTERED WHILE READING BONDS FROM PSF FILE
- FATAL ERROR: Error in QM-MM bond assignment (NAMD-ORCA)
- FATAL ERROR: Error in QM-MM bond assignment; bonded QM atoms with occupancy=1
- FATAL ERROR: Error running command for QM forces calculation
- FATAL ERROR: Error running command for QM forces calculation.
- 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: must have same number of LP hosts as lone pairs
- FATAL ERROR: PBC
- FATAL ERROR: Periodic cell has become too small for original patch grid!
- FATAL ERROR: UNABLE TO FIND BOND PARAMETERS FOR CG2O4 CG311 (ATOMS 1220 1222)
- FEP calculations - membrane protein
- Fep setup membrane protein-Drug complex
- FEP/λ-REMD Simulation error
- Files from "Hands-on" Workshop on Structural DNA Nanotechnology at Urbana
- Flat-bottom harmonic position restraints using colvars
- flexible fitting for helical structure
- Force constant for Umbrella sampling and WHAM
- Force field for Li-ion batteries electrolytes based on ionic liquids
- Force Field Parametrization
- Forces in QM/MM calculations
- Format of 'dcdfreq' field in conf file
- Formation of nanoparticle ligand complex
- Free Energy Pertubation simulation set-up
- Free energy plot
- Free-energy of association of transmembrane helices
- FW (1): 71i
- Fwd: About changing charge/multiplicity during QM-MM
- Fwd: Bypassing MM parameterization of ligand in QMMM
- Fwd: Colvars Orientation Question
- Fwd: Error: Number of NGauss expected in AddNewGTOs
- Fwd: FATAL ERROR: Charge placement error in QM-MM bond.
- Fwd: fatal error: error in qm-mm bond assignment
- Fwd: GaMD config file
- Fwd: Gromacs to Charmm FF Format Conversion -Reg
- Fwd: Inquiry regarding benchmark simulations
- Fwd: namd on AWS
- Fwd: QM-MM NAMD-ORCA broken symmetry
- Fwd: QMMM param issue
- Fwd: Running NAMD on Linux Cluster
- Fwd: running NAMD with AMBER inputs
- Fwd: Tuning QM-MM with namd-orca on one cluster node
- GaMD config file
- gamd restart file in namd 2.13
- GaMD with nucleotides
- gaussian aMD with iE=2 (setting E threshold at maximum)
- GBIS parameters
- Getting high performance on multi-copy (replica) GPU simulations
- Getting the topology,PSF files
- GLA (γ-carboxyglutamic acid) topology for CHARMM36
- GolP-CHARMM
- GPU Acceleration and Drude Simulations
- Gradual minimization
- Graphene psf file
- Gromacs to Charmm FF Format Conversion -Reg
- H2 Topology and Parameter files
- Hamiltonian Replica exchange configuration file
- Harmonic restrains
- harmonic-restraints/colvars
- hbond restraint simulation
- heating
- Heating problem for protein/ligand complex
- Hi
- Homologous structure as stating flexible fitting model
- How are the virial related variables passed from GPU to CPU memory?
- How can I analyse QMMM log file?
- How do I add passivated H-atom to ZGNR
- how does NAMD know which residue to (de)couple
- how i can utilize 4 GPU in simulation with poor performance
- How to avoid producing a huge DCD file?
- How to best use GPUs
- How to determine the residue of qmLSSRef in QwikMD?
- how to disable the periodic condition tracking two atom distance
- How to extend an ABF simulation ?
- How to fix mutex error
- How to integrate multiple walkers 2D metadynamics results?
- how to make a .Dx file trajectory to showing the Electrostatic Maps or ion concentration video?
- How to protonate GLU
- How to restart a FEP simulation
- how to run flexible fitting for structure with helical symmetry
- How to Selectively Scale Interactions
- how to set the input file for the free energy calculations with CHARMM Drude force field
- how to switch off hydrogen bonds in TIP4P/2005 water
- how to translate a protein without unfolding
- How to treat electrostatics in crystal lattice MD simulation
- Hybrid AA/CG for a transmembrane protein system
- Hybrid Coarse Grain/ all atom simulation in NAMD
- Hydrogen bond energy for TIP3 water
- Hydrogen Mass Repartitioning
- Hydrogen mass repartitioning and 4-fs time steps in NAMD
- I frequently get FATAL ERROR: Unable to open text file clc_test.equil.1.colvars.state: File exists when running across multiple nodes
- IMD simulation
- Immediate postdoc opening in Bio-molecular simulation, University of Alberta, Canada
- Implicit MD is slower than explcit MD!
- Incorrect restarting velocities
- info about gpu hardware
- inputPrefix merge error ABF
- Installation with tcl
- Ion concentration and aggregation problem of the nuclear protein simulations
- Is there a way to stop a MD run before the END_OF_RUN timestep?
- Is there someway to render protein picture without background color?
- Issue about replica-exchangeumbrella sampling by 16 threads
- Issue in reading the soluteScalingFile for REST2
- Issue regarding to the speed of QM/MM
- Issue With CatDCD in Dynamical Network Tutorial
- Issue with preparing QM-MM
- issues with QMMM and parameters
- Issues with vdW for non existing atom
- Job submission error for NAMD-2.13 ( version netlrts with cuda-10.0) using Torque job scheduler
- JS plugin issues when constructing large systems
- Langevin dynamics and random seeds
- Large number of simulations in parallel using replica exchange.
- Lennard-Jones Potential
- LIE protocol in QM/MM
- Ligand coated Silver Nanoparticle.
- Lipids generated by VMD could not use "coordpdb" to read
- log file
- looping on multiple dcds in namd configuration file
- Low simulation speed with 24 processors
- Machinefile Question
- mail about cuda exculssion count
- mail about error in configuration files
- MAIL ABOUT INTRODUCING NEW residue
- mail about pbs script
- mail about tcl script
- 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
- Maximum Timestep for NAMD
- MD simulation of a molecule with a halogen
- MD Simulations with GROMACS/NAMD/AMBER/VMD: Seasonal School in Stockholm 10-13 June
- MD with 3-site CO model
- MD without water - Reg
- MDFF chirality restrain error - measure imprp: empty atom index
- mdff for EM map with helical symmetry and the asymmetric unit is dimer
- Measuring Kinetic Energy of Solvent
- Membrana-protein-lig protocol
- Merge File Question
- minimise in restarting first equilibration step
- Minimization Error
- Missing frames in DCD header when continue from segment without DCD output
- mistakes in the user guide in the accelerated MD section ?
- MM/QM with namd
- model with TIP4 water minimization getting crashed every time
- modelling an aqueous solution of protein+hydrogen peroxide
- Modifying LJ Potential -Reg
- MOPAC output file analysis
- mpi with NAMD
- mpirun was unable to find the specified executable file
- MSM grid values
- Multi canonical ensemble method
- Multi-node job errors
- Multiple Constraints Equilibration
- multiplot: Data vector empty, ignoring plot!
- Namd
- NAMD 2.14 fatal error executing tcl script
- NAMD 3.0 alpha, operating system requirements
- NAMD configuration file
- NAMD configuration file error
- NAMD CUDA specification
- NAMD Developer Meeting 2019
- NAMD doesn't use my CUDA enabled GPU
- NAMD error : alloc_mempool_block: posix_memalign failed
- NAMD job takes long time to finish 1 ns equilibration
- NAMD on 24 threads
- namd on AWS
- NAMD on Windows 10 with huge performance drop after 39 CPUs
- NAMD overestimates the hydration free energy with Drude force field
- NAMD performance
- NAMD QM/MM multi nodes performance bad
- namd QM/MM on oak ridge ANDES cluster
- NAMD QM/MM simulations
- NAMD support for lone pairs
- NAMD took more than 1 day on 36 cpu to complete 1ns simulation for a 77000 system
- NAMD trajectory with MMPBSA.py
- NAMD with infinite cutoffs?
- namd-l digest V1 #2923
- namd-l digest V1 #2927
- NAMD-QM/MM TUTORIAL: Atoms moving too fast error
- namd3 on centos 6
- NAMD3 segfault while writing restart files
- NAMD3: how to get the best performance in one gpu node?
- namdEnergy empy output file
- namdEnergy execution issue -path for namd2 in server
- NamdEnergy Nonbonded H-bonds
- namdstats.tcl problem
- nan (Not a number) error in meta-eABF simulation
- NAN in output of aMD
- need help in study the effect of mutation,
- Need help with errors in REST2 sample file
- Need help with psfgen : psfgen can't read file.pdb
- Negative Forces in SMD Simulations
- New version of Molefacture -small molecule modeling tool- posted
- NGRP NST2
- Non bonding energy calculation through NAMD
- Non-SLI GPUs in NAMD
- not getting NAMD multicopy simulation started
- npt simulation where only one of the dimensions is fixed
- NPT then NVT simulation in a single config file for water box?
- Number of QM Atoms Error
- obtaining the viscosity of mixture from NAMD output file
- OPC Water Model
- Optimum time for md run in i3 laptop
- ORCA NAMD Parallel
- ORCA Orbital Bug
- orca_plot asking .xyz file from QM-MM
- Order of Minimizing/Heating/Equilibrating
- Orientation Colvars Question
- Output of harmonic restrains effect in alchemical route of protein-ligand binding free energy calculation
- Pair interaction calculation is not supported in CUDA version
- Pair interaction calculations of the QM/MM system
- pairlist question
- Parallel Simulation Question
- Parameter and Topology File Question
- Parameter Optimization Advice
- Parameters and topology files regarding arsorite(ASO3 - - -)
- parameters and topology for Deacylcortivazol (DAC)
- Parameters for molecular N2
- Parametrization of zinc ion (+2) in using CHARMM force field.
- Patch bond not formed
- patch for cystein bond
- patch for threonine (THP2).
- Patch grid too small error in first production run
- path CV
- pbc correction for nve unwrap trajectory aiming calculation of diffusion coefficient
- PCA calculations
- PDB structures of peptides
- Performance on GPU
- performing SMD in Z using colvar module
- Periodic boundary condition
- PhD Position In Computational Structural Biology Of Membrane Proteins
- Phosphotyrosine Parameters/Toplogy
- PME in PairInteraction Calculations
- PME with Implicit solvent - Reg
- PMF calculation
- Pointcharge file in QM/MM setup with ORCA
- position restraint only certain residues during minimization
- Possible issue with NAMD_2.13_Linux-x86_64-multicore-CUDA version for Drude support
- Post processing NAMD trajectory
- Postdoc Position at Penn in Chromosome Modeling
- Postdoctoral opening at MSU
- POSTDOCTORAL POSITION at CFM/MPC (Donostia, San Sebastian - SPAIN)
- 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++
- Prevent DNA denaturation
- Problem
- Problem in Running CUDA-Enabled NAMD Via MOE software
- Problem with BEUS in NAMD 2.14
- Problem with compiling vmd from source code
- Problem with namd 2.13 constant pH molecular dynamics, HSD residue.
- problem with solvating a structure
- problem with TIP4P on nightly version
- Problems in sharing of replicas in REMD
- Protein Charge
- Protein Deformity in Implicit Solvent Simulation
- protein movement
- Protein-ligand complex
- Protein:ligand standard binding free energies
- Protein:ligand standard binding free energies clarification question
- Protocol share Ribosome
- PSF for Cyclic-Branched Peptides
- psf generation
- psf generation for multiple trehalose molecules
- psfgen error protein-ligand
- Psfgen, Disulfide Linkages, and the Drude Polarizable Force Field
- Pulling only one half of a harmonic restraint
- Python Wrapper Bug
- QM atom cannot be fixed in space
- QM-MM and transition elements
- QM-MM NAMD-ORCA broken symmetry
- QM-MM with MOPAC
- QM/MM error in the charges
- QM/MM error: The number of QM atoms received is different than expected
- QM/MM internal energies
- QM/MM simulations with live solvent
- QMMM 1 Node vs Multinode
- QMMM Frequency Calculation
- QMMM ORCA Error
- QMMM param issue
- QMMM Question
- qmmm simulation and question for md analysis
- Quary resgading Adaptive biasing force
- Query regarding 'Protein:ligand Standard Binding Free Energies' tutorial
- question
- Question about colvars
- Question about PBC and RMSD
- Question about PMF calculation
- Question about QMMM simulation
- Question about Radius of hexagon;
- question about SMD
- Question Colvar o tclforces
- question to run namd2 with multiple CPUs
- Questions about soluteScalingFactor in REST2
- QwikMD Error: child killed: unknown signal
- QwikMD--ERROR) Unable to ascertain relative endianness of remote machine
- RAMD seed number
- Rattle algorithm error: when to minimise
- RDF of hydroxide ion in a water box
- readmol2 warning: non-unique atoms were renamed.
- Receptor-ligand binding energy from QMMM
- Reduce verbosity during minimization
- Reg: Docking
- Reg: Force Field file
- reg: quenching NAMD trajectory
- Reg: Solvation box
- Regarding "lossiness" of namd on GPUs
- regarding constant PH simulation
- Regarding FICOLL 70 & PEG20000
- Regarding Hard sphere
- Regarding number of water molecule
- Regarding PCA
- Regarding psf generation
- Regarding to the parameters of QwikMD
- reinitatoms
- Reload molecular topology for amber files?
- REMD Problem
- REMD using remote GPU
- Reminder NAMD Developer Meeting 2019
- renumbering and rewriting a trajectory
- Replica exchange on GPU with OPA network and Slurm
- Replica exchange problem
- Repulsive wall potential or spherical boundry conditions
- Research Programmer for VMD/NAMD at UIUC
- REST and Periodic Cell Issues
- Restart Annealing
- restart file
- Restarting aborted NAMD run
- restarting Gaussian accelerated MD fails
- Restarting QMMM
- restrict atoms to cross a boundary
- Resuming / Resubmitting RAMD simulations on a HPC
- REUS
- rigid body simulation with NAMD
- rmsd
- Rmsd calculation
- rmsd colvar
- rmsd colvars atom definition
- 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 ?
- Run NAMD without GPU
- Running broken-symmetry with namd-orca
- Running MD simulation for two molecules
- Running multiple walker metadynamics on Stampede2
- Running multiple walker metadynamics replicas as a bundle
- Running NAMD - 2.14 - SMP - Verbs - CUDA
- 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 multiple nodes
- running pair interaction analysis multiple dcds in sequence in single run
- Running QM-MM MOPAC on a cluster
- Running QM-MM multinode
- Salvation of non-orthogonal box
- Same timestep for my simulation run is coming more than once and in random order in the log file
- scripts to generate initial boxes of solvents
- Segfault during NAMD compilation with GCC 8.3
- Selected cofactor in final output
- Sending REUS simulations to Stampede
- Senior Investigator/ Investigator Position (Molecular Dynamics) at Silicon Therapeutics
- Senior Investigator/ Investigator Position (Quantum Mechanics) at Silicon Therapeutics
- Setting up / Running NAMD on HPC
- Setting up QM-MM with homotrimer
- Several issues (possible bugs) in REST2 - soluteScalingFile & langevinTemp
- shifting of ions from -z to +z in a single frame(1ps)
- Should a pairlist warning concern me?
- simulated annealing
- Simulation Crash SMD Coarse-Grained
- Simulation crashes during annealing the reverted all-atom structure
- Simulation of sodium dodecyl sulfate
- slow down when running 2 simulations on 1 node
- Slow performance over multi-core processor and CUDA build
- SMD for understanding the proximity of two atoms
- SMD negative forces
- SMD on Intermembrane Helices
- SMwST RATTLE Algorithm
- solute scaling does not affect electrostatics (and other quirks)
- Solvate with methanol and acetone using free energy methods in NAMD?
- solvating silica
- solvation with SWM4 water model
- Solvent Heating with Rigid Bonds
- Some questions about restrained-ensemble molecular dynamics (reMD)
- Specifying a pull direction with COLVARS
- spontaneous binding pathway with PMF calculation?
- Stability issues with POPC membrane using Drude force field
- Standard binding free energy protein-ligand (ABF)
- Standard Error Calcuation
- Stochastic velocity rescaling for Free Energy calculations
- strange benchmark results -- how would you explain them and what would you advice?
- String Method with Swarms of Trajectories (SMwST) Performance
- Support for drudeNbthole on CUDA version of NAMD
- Support of recent Amber force field
- Swarms Errors
- Swarms of Trajectrories MPI NAMD Run
- System Drifts Along Z-Axis
- Targeted MD in NAMD 3.0?
- Targeted molecular dynamics domain selection question
- TclBC forces on individual atoms
- Technical specifications for the V100 and GTX gpu cards
- TeraChem
- TeraChem QMMM
- Termination between Minimization to Equilibration
- The best initial structure of Protein-Protein complex
- The HIP version of NAMD gets wrong results when computing on more than one node
- Thermodynamic Integration document
- TI alchemical transformation of a ring atom: small partial charge difference affects strongly dG
- TIP4P water box
- TMD config parameters
- TMD Partial Fitting Problem
- TMD questions - refined
- Topology and parameter files for flavonoid compounds
- toppar_water_ions.str NAMD format for last version of C36 (on July 2020)
- Transforming ORCA data to CHARMM format
- Transition State Search BY NAMD
- Tuning QM-MM with namd-orca on one cluster node
- Tutorial
- Umbrella Sampling in PLUMED + NAMD
- Umbrella sampling of a protein through a membrane
- Umbrella sampling of AA and CNT dissociation, pmf doesn't flatten & reduces over large distances...
- Unable to calculate SMD for amber topology
- unable to open restart.colvars
- Unit of Force constant of position restraint
- Unpredictably Crashes upon Restarting
- use Colvars to track four group of pair atoms distance at same time?
- Using amberFF and NAMD
- using an Amber topology with OPC water model in NAMD
- Using harmonic walls on water molecules
- Using NAMD and Orca together -- a QM/MM job
- Utilising the GPU in NAMD((NVIDIA CUDA acceleration) in windows
- vacuum simulation -Reg
- veccross implementation in tclforces
- vecsub:two vectors don't have the same size
- Velocity MAP calculation in VMD
- Velocity unit
- VMD nc file problem
- vmd-l: Bugs and Questions
- vmd-l: Getting the topology,PSF files
- vmd-l: NAMD and VMD Armv8-A
- vmd-l: ORCA Orbital Bug
- vmd-l: Pair interaction calculation is not supported in CUDA version
- vmd-l: PDB structures of peptides
- vmd-l: PME boolean
- vmd-l: query on how to allow the protein to interact with the water molecules
- Warning: DUPLICATE ANGLE/BOND/DIHEDRAL ENTRY FOR ...............
- Water Molecule Issue
- Water wrapping in the QMMM simulations
- we apply a harmonic potential
- well-tempered metadynamics deforms the water box and the system becomes unstable..
- WHAM
- what's the latest on using NAMD (and MD in general) for docking?
- When to use a semicolon in a *.conf file?
- When using WHAM TO ANALYSIS
- Why very large force reported at the starting point of constant velocity SMD run in NAMD log file?
- Workshop on Free Energy calculations in Muenster March 11-13 2020
- Wrong number of basis-sets stored!
- Wrong result in running QM/MM simulation with a small test system
- xMDFF Error
- Zero PME pencils found
Last message date: Thu Dec 31 2020 - 22:29:33 CST
Archived on: Thu Dec 31 2020 - 23:17:15 CST
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