NAMD-L: By Subject
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About this archive
Starting: Sun Jan 01 2017 - 04:00:35 CST
Ending: Mon Dec 31 2018 - 09:42:31 CST
- "'Hands-on" Workshop on Computational Biophysics at Pittsburgh, PA, May 21-25, 2018
- "block" module for NAMD
- "Child killed: segmentation violation" error when running QM/MM minimization in QwikMD
- "Hands-on" Workshop on Enhanced Sampling and Free-Energy Calculation at Urbana, IL
- "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
- "Periodic cell has become too small for original patch grid!" with membrane system on GPU
- (1) Failure running QM-MM with ORCA and (2) problems preparing input with transition metals
- (no subject)
- ++idlepoll
- -nan values and fatal error
- 1-D ABF and Compressibility
- 2.12, cufft problems on a GTX 1070 ?
- 2.12, cufft problems on a GTX 1070 ? [SOLVED]
- =20=20none?= quilibrium SMD with fixed atoms
- [ REST2 ] Possible bug on NAMD example
- [NAMD] Apply an electric field only in a specific region
- [NAMD] Define time-dependent grid force
- [NAMD] File Missing in Nanopore Tutorial
- [NAMD] How to build and simulate a periodic DNA in NAMD
- [NAMD] Obtain dynamical matrix away from equilibrium
- [NAMD] Outputting PMF at half the time using Metadynamics
- [NAMD] Patch 5MC2
- [NAMD] Problem with colvar "tilt"
- [NAMD] Question about patches
- [NAMD] Running NAMD in Stampede2
- [NAMD] Running REUS in many nodes
- [NAMD] Simulations in guanidinium chloride
- [NAMD] Too many collective variables?
- [NAMD] Units of Efieldfreq
- [NAMD] Using ABF to study separation of two molecules
- [NAMD] Using as collective variable the minimum of a set of distances
- [VMD-NAMD] Question about Dipole of DNA / Dipole Moment Watcher Plugin
- A problem in ABF simulation
- ABF Asymmetry
- ABF FEP with multichain receptor
- ABF for dihedrals
- ABF Question
- ABF Questions
- ABF simulations with singularities?
- ABF vs Umbrella Sampling entrance barrier heights discrepancy
- ABF Window Boundaries
- ABF with alpha colvar?
- ABF, rigid bonds and constraints
- ABF: umbrella_int.awk
- about colvar module in NAMD
- About CUDA version
- about GaMD reweighting
- About the performance of RAMD
- About the robustness of ABF and FEB protein-ligand
- accelMDbdihe is not working properly in NAMD after commit e3e849639982dcba9a60c6072c81fdb7cba69759
- accelMDdihe is not working properly in NAMD after commit e3e849639982dcba9a60c6072c81fdb7cba69759
- accepter
- acceptor
- adaptive biasing force
- Affinity
- Alchdecouple for dihedral/improper terms
- Alchemify?
- all-atom to coarse-grained system
- Amber force filed input failure on GPU
- AMBER NetCDF file for Simulation
- analyze NAMD trajectory in Curves+
- Angle of lone pair in TIP4P 2005 simulation
- applying constant force on water molecules in a particular direction
- Are KNL a good choice for classical MD?
- 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 selection error
- Atom velocity error in coarse grained simulation using MARTINI
- Atoms too fast/periodic cell too small with ABF protein-ligand
- AutoPSF Error
- AW: ++idlepoll
- AW: Are there plans on thermostat groups?
- AW: Aromatic rings don't maintain the planarity during the heating
- AW: AW: AW: not a number in NAMD log file
- 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: NAMD-2.12 CUDA2 and PMECUDA problems
- 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: building system with or without water for metadynamics
- AW: Change pressure during simulation
- AW: Difference between REMD replica temperature and actual temperature
- AW: FATAL ERROR: ERROR(S) IN THE CONFIGURATION FILE
- AW: High pressure calculations
- AW: How to run a TCL proc at every step in NAMD using callback command?
- AW: Hydrogen Mass Repartitioning in NAMD
- AW: Low global CUDA exclusion count! (9592 vs 9618)
- AW: Movie in VMD
- AW: NAMD performance monitor
- AW: NAMD SMP version warning - Reg
- AW: NAMD-2.12 CUDA2 and PMECUDA problems
- AW: NAMD-2.12 handful of issues with CUDA
- AW: not a number in NAMD log file
- AW: Organic Solvent & Water Simulation
- AW: Periodic cell has become too small for original patch grid
- AW: question about GPU
- AW: REMD on HPC
- AW: Scaling behaviour of NAMD on hosts with GPU accelerators
- AW: Scaling behaviour of NAMD on hosts with GPU accelrators
- AW: Solvent box fluctuations
- AW: vmd-l: Building NAMD 2.12 from Source with IB and CUDA
- AW: Weird PBC wrapping
- Bad global bond count! (48842 vs 48843)
- Bad structure after converting the coarse grained last frame to all-atom
- basis set for QM-MM dft
- Best NAMD distribution for COEUS cluster?
- Best water model
- Better way to fix the atom -Reg
- Bias-exchange metadynamics
- Binding free energy tutorial
- Bond parameter error for the system which has been converted using residue-based coarse-grained method
- Bond-jitter/Total-energy-spikes during energy minimization in vacuum
- bpti example compiled source charmrun++ does not launch
- Broken Structure after reverting coarse-grained system to all-atom system
- Bug with FEP?
- BUG: ReplicaUniformPatchGrids and "output" command namd-2.13NB
- Build for CUDA support
- Build NAMD with CUDA for unix workstation (centos 7)
- Building namd 2.12 from source an ARM64 architecture
- building system with or without water for metadynamics
- Building with GCC on Ubuntu 18
- C36 force field
- calculate cumulative dG
- Calculate energy of a residue using NAMD energy
- Calculating electrostatic force from NAMD trajectory
- Calculating gradient of the potential (force field) on each atom.
- Calculating hydrophilic and hydrophobic Solvent Accessible Surface Area
- calculating non bonded energy using namdenergy
- Calculation of Diffusion coefficient
- calculation of helical axis in NAMD
- Can large number of atoms define in colvariables reduce the computational speed in adaptive biased force (ABF) simulation via lowering the GPU utility?
- Carma/grcarma v.1.7 released.
- Cascade MDFF
- Center of mass drift
- CGenFF 4.1 lone pairs
- Change pressure during simulation
- Charm++ Fatal Error Question
- Charm++ fatal error with QM-MM MOPAC
- Charm++ supports RoCE ?
- CHARMM FF parameters for FE-S bond in CYP450
- charmm parameters for buffer molecules
- CHARMM36 parameters for nucelobases
- CHARMRUN ERROR
- Choice of bromide ion LJ parameters
- Cleaving and capping protein with autopsf leads to parameter errors upon running NAMD
- CMIAbort Error
- Coarse Grain of a Calcium Binding Protein
- Coarse Grained simulation of silicon nitride nanopore - Reg
- coarse-grained simulations with errors "Atoms moving too fast" and "low global exclusion"
- Coarse-grained umbrella sampling for POPS-protein system
- Collective variable remains at zero during Umbrella Sampling
- Colvar distance xy to restrain ions
- colvar distanceInv not propagated with a harmonic moving restraint in NAMD 2.12
- Colvar Error
- colvar with moving frame of reference
- Colvars alternative recommendations
- Colvars and distance restraint for umbrella sampling
- colvars not scaling well in NAMD 2.10
- Colvars Restraint Question
- colvars selecting frames
- colvars to restrain peptide close to lipid
- Colvars wall boundaries for CoordNum
- colvars/rmsd: Error: definition for atom group "atoms" not found.
- colvars: Did the orthogonality requirements of colvars change in ABF?
- colvars: Error: Feature unavailable:compute total collective force only from one group center
- colvars: Error: keyword "translatereference" is not supported, or not recognized in this context.
- colvars: How to implement a collective variable of vector type?
- colvars: keepFreeEnergyFiles doesn't work in latest colvars version
- colvars: make an extended CV periodic
- colvars: Questions about the metadynamics hillWIdth option.
- compilation of NAMD 2.12 fails
- Compiling charm/NAMD with an alternative gcc, e.g. gcc 6.x
- Compiling NAMD on stampede 2.
- Concatenate Outputs
- Concatenating log files
- Configuration of new HPC Cluster for NAMD and GROMACS
- Constant Force Pull
- constant temprature for vacuum condition in namd file
- Constrain on DNA when using ABF for protein-DNA system
- Constraining and imparting motion to a geometry
- Constraining bonds that aren't hydrogens - splitPatch usefulness ?
- Constraining bonds that don't include hydrogens
- Constraint failure in Highly charged system - Reg
- Consulting about buying new hardware (GPU)
- Continuing metadynamics run
- Continuing SMD from restart files
- convergence criterion of free energy perturbation (FEP) simulations for pKa calculation
- convert a 3d system into a 2d system
- Converting a mixture system from NAMD to LAMMPS
- Converting GromacsForce File to NAMD using GromacsTopFile.C
- Converting x,y,z coordinates to dcd file
- Couldn't open DCD file
- CPU/GPU energy difference
- Creating an infinite graphene sheet
- Creating psf file DNA
- Creating psf file for ligand
- creating topology for a unique structure
- Critical isofrom selectivity in molecular dynamics
- Cross-term (CMAP)
- cuda errors when running NAMD
- Custum made residue addition
- Cutoff radius for electrostatic embedding in QM/MM calculations
- CZAR Estimator: grad file
- dcd to pdb conversion
- Decreasing performance of cluster running FEP
- Define a colvar from other colvars
- Define spheres using NAMD
- Defining colvars based on a region
- Defining custom Colvars to measure pmf with Umbrella Sampling
- detecting vanishing atoms in zero.fep
- Dielectric Constant in the gas phase
- difference between .vel and .vel.restart
- difference between constraining,restraining and fixing the atoms
- Difference between REMD replica temperature and actual temperature
- Different cell vectors - Reg
- Different resid in pdb fie but showing same molecule in VMD
- Diffusion Coefficient calculation
- Dihedral colvar
- displacement of protein
- distance filter during data analysis
- Distorted peptide bond with new residue
- DNA capping
- Do firsttimestep, numsteps and run have maximum values?
- Does FEP really run on Knights Landing?
- Double-defined segid, resid for more than 9999 id's
- Downloads are .tar files but have .tar.gz extension
- Drude minimization does not converge
- 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
- eABF - Fullsamples and windows merging
- effect of acceptors
- Electric field simulation: eFieldNormalized
- electric field- forces in NAMD source code
- Enabling charmrun in NAMD simulation
- energy calculation with namdenergy
- energy difference between HSE and HSD
- Energy Gradient Plotting
- Energy Minimization failure for mutants
- Energy values
- Enhanced Sampling and Free-Energy Calculations Lectures
- Enhanced sampling methods for oligomers
- Enhanced sampling of domain motion and gsafold
- enhanced sampling of domain motion, GSAfold
- enhanced sampling of flexible tail
- Equilibrated TIP4P_2005 Waterbox
- Equilibration in NPT simulation
- Equilibration of membrane water system (pressure in NVT)
- Equilibration using NPT and Production run using NVE ensemble
- Equilibrium Energies
- error - atom type not in psf
- error - parameter file for fluorine on a benzene ring
- Error : components of colvar "alpha" does not support system force calculation
- error during minimization
- Error during simulation
- error in (runfepmin)
- ERROR in multiple walker metadynamics simulation
- Error in NAMD Simulations -Drude
- Error in the Continuation TMD simulation Run.
- Error in thermodynamic integration for calculating ligand absolute binding free energy
- Error NPT simulation - Need Urgent Help - Reg
- Error on Settle.C when compiling NAMD with Intel Compiler
- Error Regarding minimization
- Error regarding missing angles between perturbed groups for fep calculation
- Shannon, Gareth Bayley. (ARC-SS)[UNIVERSITIES SPACE RESEARCH ASSOCIATION] (Fri May 26 2017 - 17:03:36 CDT)
- ERROR TOLERANCE
- Error with D-amino acids mid-sequence using NAMD 2.12/2.13b2 and CHARMm36
- Ewald size-dependence correction in FEP simulation of an electric dipole
- excluding ions based on mass
- Explanation of parameters for NBTABLE's tabulated external file?
- extracting avarage pdb from dcd file
- extracting force on a single atom
- facing problem while downloading NAMD
- FAD parameter and topology files
- FAD topology and parameters
- Fatal Error in NAMD
- fatal error in running namd/2.12
- Fatal error in the simulation of a water box
- FATAL ERROR running apoa1 with NAMD 2.12
- FATAL ERROR: Bad global improper count!
- FATAL ERROR: cuda_check_progress polled 1000000 times over ...
- FATAL ERROR: Duplicate bond
- FATAL ERROR: Duplicate bond when going from nvt to npt
- FATAL ERROR: ERROR(S) IN THE CONFIGURATION FILE
- FATAL ERROR: Singular matrix in routine ludcmp
- FATAL ERROR: Unable to access config file temp14.conf
- FATAL ERROR: UNABLE TO FIND BOND PARAMETERS FOR CG321 CTL3 (ATOMS 8773 8776)
- 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 ExtraBonds
- FEP with intermediary segments
- FEP/REMD (ERROR: 'alchLambda' is a required configuration option)
- FFTK Determination of Dihedrals to be Scanned
- ffTK torsion scan convergence using Gaussian.
- FFtK Tutorial (Urey-Bradley angles error).
- ffTK Without Using Gaussian
- finding atoms in protein-lipid system having electrostatic interaction
- First "Hands-On" Workshop on Structural DNA Nanotechnology
- Fix aminoacids - error
- Fixing COM of one atom in selection and letting the other move
- flat and smooth energy?
- Free energy (eABF): negative RMSD and harmonic restraints.
- Free energy calculation under external bias, (e)ABF/US/etc
- Free energy did not converge by using ABF
- Free MD simulation (Production run)
- Functional role of the internal water channel within the receptor
- Functionality of wrapWater and wrapAll commands for periodic simulations
- Fwd: (1) Failure running QM-MM with ORCA and (2) problems preparing input with transition metals
- Fwd: ABF FEP with multichain receptor
- Fwd: About the robustness of ABF and FEB protein-ligand
- Fwd: About wall clock time
- Fwd: Are KNL a good choice for classical MD?
- Fwd: Atoms too fast/periodic cell too small with ABF protein-ligand
- Fwd: colvars to restrain peptide close to lipid
- Fwd: enhanced sampling of domain motion, GSAfold
- Fwd: facing problem while downloading NAMD
- Fwd: FEP & node/core number
- Fwd: FEP protein-ligand tutorial 2017 unclear section
- Fwd: FEP slowdown during execution
- Fwd: FEP with intermediary segments
- Fwd: Is QM/MM compatible with Colvars?
- Fwd: Klaus Schulten Memorial Symposium, registration and accommodation
- Fwd: Ligand atoms moving too fast with FEP
- Fwd: measuring Euler angles and polar angles
- Fwd: parameter request for PRES bonding
- Fwd: parseFEP domain error
- Fwd: ParseFEP for restating FEP
- Fwd: pressure in interfacial tension
- Fwd: Question on restraints with MM-GBSA
- 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
- g++ 5.3 fails on 2.12/2.13b1 with CUDA 8.0
- GAAMP
- GaMD in NAMD
- Gaussian Dihedral Scan Log files visualization.
- gbis for acetonitrile
- gbsa
- generating nodelist and error
- generating topology file
- Get NAMD version from the tcl script interface
- git rid of it
- Gradual cooling of the system
- Gyration in colvars doesn't work with eABF.
- Hamiltonian Replica Exchange MD in NAMD
- Handling of nonbonded lists in PSF - please clarify
- Hands-On Workshop on Computational Biophysics: April 17-21 in Urbana, IL
- Hands-On Workshop on Computational Biophysics: May 30 - June 2 in Pittsburgh, PA
- Hard wall on Z direction for ions
- Harmonic force Keyword "centers" significance
- having problem with disulfide bond
- Having problem with restarting colvar distance,
- High pressure calculations
- Holding molecules on one side of membrane
- how do I restart umbrella sampling calculations?
- How does NAMD calculate AccumulatedWork when using RMSD colvar?
- How to add a C code to NAMD properly?
- How to calculate 2d surface energy surface on segmented adaptive biased force (ABF) simulations
- How to calculate free energy to unbias colvars restraint?
- How to calculate the number of solvent molecules for simulations in a specified pressure
- How to create multiple molecules using psfgen
- How to define spheres of different sizes and their spatial constrains using NAMD?
- How to get 3D figure of solvent accessible surface area from APBS output
- How to get ideal alpha-helical, ω-shaped γ-turn, and turn/310-helix conformations
- How to get the right density of a methane system
- how to have large coordinate values in the "coordinates PDB" file
- How to interpret Thermodynamic Integration output
- How to make water stay in the Z direction?
- How to perform REMD of a system a membrane-protein system?
- How to pull protein-Monomer from DNA using ABF without any force on DNA?
- How to restart metadynamics in namd
- How to run a TCL proc at every step in NAMD using callback command?
- How to sample pressure from NAMD log file.
- How to set setting periodic boundary condition
- How to set the configuration file for a NVE simulation
- 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)?
- Howto gaussian accelerated MD
- Hybrid QM/MM in NAMD 2.12 with Gaussian
- Hybrid QM/MM NAMD: Problem Reading Extended psf files -- But some good news too
- Hydrogen Mass Repartitioning in NAMD
- Hydronium parameters
- I don't have any eabf output file.
- Implementation of sortreplicas executable for restarted REST2 simulations
- Implicit solvent no non-bonded pairing
- Improper section for parameterization
- Included Topology (.itp) in gromacs to parameter file for NAMD
- Inconsistency between NAMD 2.11 and NAMD 2.12
- Incorporate aluminum oxide monolayer
- Induced Electric filed and Electrostatics - Reg
- Info on solutescaling
- introduction to research on free energies
- ion moving laterally during Umbrella Sampling?
- Ion type in NAMD Implicit solvent model for ionizing the system
- is NVE ensemble for production run justified?
- 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?
- Isomerization between runs
- Issue using qwikMD with an uncommon cofactor
- Issues about Keep_water_out.tcl acript
- Jobs and Evens in CHARMM-GUI
- Keeping potassium ions out of an area during equilibration
- Kinetic energy outputs
- Klaus Schulten Memorial Issue (http://pubs.acs.org/toc/jpcbfk/121/15)
- Langevin Dynamics Coefficient Value -Reg
- Ligand atoms moving too fast with FEP
- Lipid bilayer and ligand interactions
- Lipid bilayer deformed during coarse grain simulation
- lipid centering
- Lipid_bilayer_area_per_lipid_problem_using_NPT_CharmmForcefield
- long simulation and error "integer value too large"
- Low global CUDA exclusion count! (9592 vs 9618)
- Lowe-Andersen Thermostat Speed
- Magnetic field
- mail about autoionize plugin
- mail about constraints in namd configuration file
- mail about error in namd compilation
- Mail about force field parameters
- MAIL about namd velocity error
- mail about non bonded parameters
- mail about usage of water tcl script in membrane
- Mail from vidhyasankar
- mail reg constraint force
- mail reg membrane tutorial
- mail reg Namd compilation
- MAIL REG NAMD PBS SCRIPT on mpi cluster
- Maintaining PBC on Collective Variables
- make psf error for ligand
- making glucose chains using charmm36
- margin and pressure in CUDA version
- Martini CG parameter errors for lipids
- MDFF simulations in membrane environment
- Meaning of warning in output log file
- measuring Euler angles and polar angles
- Membrane Simulation
- merging abf trajectories with different number of colvars
- metadynamics problem
- metadynamics reaction coordinate
- metadynamics run in NAMD or using plumed in NAMD
- Metadynamics simulation
- Metadynamics state file
- Microtubule Simulation
- minimization
- minimization error
- Minimization Question
- minimizing each structure of a DCD file
- minimum CUDA compute capability required for NAMD2.12
- Mismatch in atom number between psf and dcd files
- missing binary operator before token "("
- Missing cphrst file
- Missing Parameters For H3O+
- missing parameters.
- Molecule-based Electrostatics Cutoff?
- MOPAC Plugin Update
- MOPAC Point Charges
- More FEP using separated topologies
- Movement of chloride ions during MD
- Movie in VMD
- MPIRUN SLURM SCRIPT
- mscs.pdb
- Multi-dimensional PMF
- multi-node mpiexec issue
- Multiple Colvars
- Multiple Electric Field simulation
- multiple replicas metadynamics
- namd 2.12 and plumed 2.3
- Namd 2.12 error with Nvidia M2090 cards
- NAMD 2.12 multicore CUDA on Ubuntu 16.04 with NVIDIA Tesla M10 produces segmentation fault
- NAMD 2.12 using CUDA 8.0
- NAMD 2.12 Volta Compatibility
- NAMD 2.13 and RTX2080Ti
- NAMD Acceleration using P100 (GP-GPU) accelerator
- NAMD compiling problem
- NAMD crashes when Multilevel Summation Method (MSM) is on
- NAMD DCD file format
- NAMD developer workshop - Chicago, May 22-23, 2017
- NAMD developer workshop at Chicago IL, May 22-23, 2017
- NAMD Developer Workshop at Urbana IL, June 11-12, 2018
- NAMD energy run in VMD
- NAMD Error
- NAMD for Stampede2
- NAMD hangs at "Load balancer assumes all CPUs are same." when runs on an infiniband cluster.
- NAMD job termination
- namd mpi
- NAMD on Stampede 2
- NAMD on UCSD Comet
- NAMD performance monitor
- NAMD QM/MM
- 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 with multiple molecules
- NAMD+PLUMED
- NAMD-2.12 CUDA2 and PMECUDA problems
- NAMD-2.12 handful of issues with CUDA
- NAMD-CUDA GPU workload
- namd-l digest V1 #2196
- namd-l digest V1 #2289
- namd-l digest V1 #2316
- NAMD/VMD installation for Windows 10
- namd2 GPU error
- NAMD2.9-ERROR: Constraint failure in RATTLE algorithm for atom!
- namd2.exe has stopped working, NAMD Energy
- namd2_ti.pl Error: Modification of non-creatable array value attempted
- NAMDEnergy with xtc file
- nan for Drude's LP in distance-like colvars
- Nano-bio interaction in NAMD
- Need help preventing hydration of the lipid-protein interface
- Need help preventing hydration of the lipid-protein using tcl script
- Negative step number
- Neutralize a box for FEP
- No minimized system after running minimization in NAMD
- non uniform attempts distribution in constant pH MD
- nonequilibrium SMD with fixed atoms
- nonuniform sampling in ABF
- not a number error
- not a number in NAMD log file
- Npt lipid simulation with electrostatics 2
- NPT simulations with PLUMED in NAMD
- NVIDIA Quadro(R) GV100 card for NAMD studies
- nvt vs nve file
- On-the-fly eABF: Problem with the tcl script.
- Optimizing namd run
- ORCA GPUs
- ORCA QMMM
- Organic Solvent & Water Simulation
- overlapping windows in ABF
- PACE CG Model
- Pair interaction energies: TCL error -reg
- pairInteraction and PME?
- pairInteraction commands
- Parallel Jobs
- parameter
- parameter file for ACE and CT3 cap
- parameter request for PRES bonding
- ParseFEP error
- ParseFEP error with FEP in segments at different lambda schedule
- ParseFEP for restating FEP
- patch
- patch ID error
- PBC and restraints
- PBC error. Amber force field in NAMD
- PCA and vector
- PDB file creation
- performance is more poor for namd 2.12
- performance of NAMD on KNL
- performance of NAMD SMP MPI version
- performance on ~1.5 million atoms system
- Periodic cell basis too small for GridForce
- Periodic cell has become too small for original patch grid
- Periodic cell too small with GPUs, not with pur CPUs
- Periodic molecules in NAMD
- Ph.D. and Post-doc positions in molecular simulations and structural bioinformatics
- Ph.D. candidate position in biomolecular modeling or bioinformatics
- Phosphorylated Residues
- pKa calculation with thermodynamic integration (TI)
- PME Tolerance
- PMF calculation using CPU and GPU
- polymer
- Positions for Ph.D. candidates in biomolecular modeling
- Positive energy for protein
- Positive energy values for protein
- Positive VDW energies
- Post-doc position at ALCF - HPC post-doc in Computational Materials
- Pressure ? High values ; Pressavg Gpressavg ? value of first step of restart very different from the last of the previous MD
- principal axes in colvars
- Problem generating pdb psf of ATP
- Problem in generating psf
- Problem in NAMD memory optimized version - Reg
- Problem in NAMD QMMM
- Problem in running wham
- problem in writing the coor files
- problem to generate LPS PSF file using PSFGEN
- problem with minimization and calculation of force on a fixed atom
- problem with minimizer
- Problem with namd2 execution on Windows GPU version
- Problem with running on multiple nodes
- Problems about constraint (conskcol) in umbrella sampling conf file
- problems mutating HID to TYR for free energy calculations
- Problems running FEP on Lenovo NextScale KNL
- problems running GPU-accelerated namd
- Problems with temperature control.
- Production run after equilibration
- Proper combination of langevinHydrogen with rigidbonds
- Proper use of psfgen "mutate"?
- Protein Penetrating Water Box
- protein stability in a membrane and SMD
- Protein trapped on an edge of the simulation cell using C36 force field
- Psf file generation with Gromacs Parameters
- psf from parmed
- PSFGEN 1.6.4 autogenerate PATCH keyword not available
- PSFgen failed to guess coordinate due to bad angle CD CG HG2
- psfgen giving wrong structure in the autopdb file
- psfgen readpsf error with no more explanation
- Pulling protein through membrane without changing the position of membrane
- Python based tool for analysis of DCD trajectories
- Q=9B=9E=E5=A4=8D:__Free_energy_(eABF):_ne?= gative RMSD and harmonic restraints.
- QM atoms outside the PBC boundary in QM/MM calculation
- QM-MM flooding potential
- QM-MM ORCA Charm++ error Could not find QM output file
- QM-MM with MOPAC
- QM/MM Error
- QM/MM MD and the qmParamPDB file
- QM/MM Parallel Computing With Orca
- QM/MM Question
- QM/MM With Mopac Error
- QM/MM with Orca: Memory allocation failed
- QMMM FEP
- qmSecProc Proper Use
- Querries on eABF
- Query for coarse grain system
- Question about "useConstantArea" in puresure control model
- Question about applying external force
- question about GPU
- Question about new NAMD QM/MM code
- question about point substitution A→U
- question about Steered Molecular Dynamics
- 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
- Questions on creating constraints in NAMD
- Questions on implementing new collective variable in colvars.
- Qwikmd ABF Question
- QwikMD Question
- QwikMD SMD force calculation
- Radial pair distribution function for internal water analysis
- raising temperature after equiliobration
- Random Velocities Question
- Rattle algorithm Constraint failure - Reg
- Rattle error with lateral pressure calculations
- RATTLE error with lipid bilayer system
- re-centering the molecule while restarting the run
- readable output of gbis.coor
- reconstructing pmf
- Reg autioionize plugin
- reg diffusion of water molecules
- Reg membrane assembly
- Reg membrane hydration
- Reg Membrane simulation
- reg nan error in namd
- REG Protein inserion in to membrane bi layear
- Reg seeting of periodic boundary condition
- regarding constant velocity steered molecular dynamics
- Regarding Error on HB2
- Regarding free energy
- Regarding free energy calculation
- Regarding Topology and Parameterization
- regarding umbrella sampling simulation
- Regarding: Free energy of alchemical transformation of K + and Na +
- Regular vs US sampling runs.
- reinitatoms
- REMD on HPC
- REMD restart tcl script meaning?
- REMD using NAMD 2.13
- Replica exchange simulation with GPU Accelaration
- replica_bias and colvars
- Requesting abstracts for MRS Fall 2018 Symposium BM03: Multiscale Modeling of Soft Materials and Interfaces
- Research Programmer Positions Available
- Residue Charges
- REST2 patch for NAMD 2.12
- REST2 simulations: Corecting shifted dcd files!
- restarting and continuing - difference
- Restarting FEP calculations
- restarting Gaussian accelerated MD fails
- restrain lateral movement during ABF
- restraining selected atom's z coordinates
- Restraining the mass centre coordinate during Umbrella Sampling
- restraints and constraints in NAMD
- Restrict drift of Graphene sheet in X-Y plane using Colvars
- Restring the coordinate during Umbrella Sampling
- reverting atoms introduced by name into standard PDB ones
- Reverting coarse-grain system to all-atom system
- RFC: shell scripts and support functions for NAMD on Slurm (including GPU and Infiniband)
- Right NAMD version
- RMSD colvar not working in NAMD2.12 Linux version
- RMSD of backbone changes rapidly at the beginning of production run
- 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 namd cuda with srun.
- Running 2.12
- Running IMD with TMD (domain restraints)
- Running multiple-replicas metadynamics
- Running NAMD on Intel OmniPath
- Running on GPU
- Running QM-MM MOPAC on a cluster
- Running QM-MM tutorial on a cluster
- Sample umbrella sampling input file
- Scaling behaviour of NAMD on hosts with GPU accelrators
- Script for Terachem QMMM
- scriptedColvarForces doesn't work in recent NAMD builds
- SegFault in QM/MM run
- Segmentation fault
- Segmentation fault during water MD
- Segmentation fault error with 'nan' pressure and energy
- Segmentation fault for the tutorial
- Selecting atoms in NAMD .conf file and time-varying electric field
- Selecting waters from dynamics trajectory
- Selective accelerated MD in NAMD
- 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
- Setting up softcore parameters for FEP
- Setting up the range for movement of protein in umbrella sampling
- Shear flow simulation setup
- Simple PME Question
- Simulating a Binding Event
- Simulating Protein Entering membrane
- Simulating Protein/Membrane interface with pre-equiliibrated lipid bilayer
- Simulating SDS molecules
- simulation becomes unstable in residue base coarse grained system
- Simulation crashes on GPU
- simulation crashing in 2nd stage equilibration
- Simulation of imprinting process in NAMD
- Simulation of the mechanical stress in NAMD
- Slurm Run on supercomputer
- Slurm Script for Multi Node Run
- SM Bargeen A Turzo wants to share the file Min_error with you
- SMD with colvar not working
- SMD: Combined Constant Velocity and Constant Force method
- SMD: constant velocity output analysis (Develop force and displacement plot)
- SMP instructions for multi-node calculation on POWER 8 + P100
- Software for molecular electrostatic calculations
- Solutescaling not working with Amber files
- Solvation free energy difference of alchemical transformation of K+ into Na+
- Solvent box fluctuations
- Some questions about the orthogonality of colvars in ABF.
- Some water molecules are missing in psf
- sortreplicas on Stampede 2
- specify H-bond in CGMD
- Specify number of water molecules:simulation set up in VMD
- Spectre/Meltdown patch performance hits
- Stack Traceback problem in colvar restrain
- Standard density -reg
- Standard Output: Benchmark vs Timing
- statistical error in ABF calculations
- Steered MD simulation with pull and rotation
- Steered Molecular Dynamics
- Strange Bond Behavior Question
- strange diffs in energy output of NAMD 2.9 vs. 2.11
- Stress calculation
- Sudden /\A drop in last FEP window
- Sudden drop of /\A in ParseFEP.log near lamda 1.0
- Surface Tension calculation
- SWM4-NDP PSF File
- Syntax for replicaRecv
- tar.gz incorrect firmat?
- Targeted MD, "Biased atoms" and "Fitted atoms", RMSD
- TCBG Live Computational Biophysics Workshop Lectures
- TCBG Workshop lecture videos
- TCBG Workshop lecture videos😝😚😚
- tcl used for binary compilation
- temperature accelerated molecular dynamics
- Temperature Fluctuations in Drude Simulations - NAMD
- the fep error in third part of config file
- the instance type selection for NAMD simulation in Amason marketplace
- The number of QM atoms received is different than expected
- The reason for the formation of bubbles in heating stage
- The use of NPT or NVT ensemble to observe dynamical parameters
- Thermodynamic integration output analysis
- Three bonds with water in vmd from NAMD DCD
- Tilting angle of lipid calculation
- TMD without alignment
- TMD: initial and targeted structure does not have same number of atoms
- Too many iterations in routine jacobi during FEP
- Too many iterations in routine jacobi.
- topology file for the residue CSO
- torsion scan
- torsional restrain
- Total charge problem
- trouble with colvars module
- Trouble with NAMD Win64-CUDA 2.12 on my new PC
- Two parameter file in NAMD configuration file
- two stage equilibration in single configuration file
- Type of solvent water molecules
- Umbrella Sampling colvar file parameters
- Umbrella Sampling input parameters
- 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
- Unable to run CUDA NAMD but able to run non-CUDA version on Windows
- Unexpected Energy values - Reg
- unit dipole moment vector
- Unusual WT-Metadynamics gaussians heights
- Update particle position iteratively in between steps
- User force field with FEP?
- Using 3 GPUs (but not 2) causes energy and temperatures to rise extremely fast in NAMD 2.12
- Using 4-site water model in NAMD
- Using center of mass to calculate the radial distribution function
- Using Gromacs topology in NAMD
- Using PBC tools for a cubic and a rectangular box
- Using restraint on the dye using radius of gyration value in namd
- vacuum condition in config file
- value of langevinTemp in case of binvelocities
- variation of pressure
- Vectors and indexing in VMD
- veldcdfile command
- velocity.pdb and velocity unit in NAMD
- verbs-smp on a single node
- very small cell
- Vibration Analysis Script
- vmd-l: 780Ti and NAMD2
- vmd-l: [VMD-NAMD] Question about Dipole of DNA / Dipole Moment Watcher Plugin
- 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: Large number of harmonic distance restraints
- vmd-l: Proper use of psfgen "mutate"?
- vmd-l: PSFGEN 1.6.4 autogenerate PATCH keyword not available
- VMD/NMAD on AWS
- Water atoms' explosion out of solvate box in my RBCG simulation on NAMD
- water box tilts during equilibration
- Water permeation through aquaporin-Z
- Water Transport
- Way to wget or curl download the precompiled NAMD?
- Ways to find water molecules passing through the water channel in lipid bilayer
- Weird PBC wrapping
- What is the exact form of the harmonic potential used by the NAMD "constraints" option?
- What NAMD version to obtain
- What to cite for CHARMM22
- Which NAMD-Build for my local HPC?
- 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?
- Workshop on Computational Biophysics, Urbana, IL: Application Deadline March 10th
- Workshop on MD simulation software design
- Wrapping multimeric protein issues
- write first point into (vel)dcd file
- Writing pdb file for a particular frame
- wrong pdb struvture generated while using patch
- xMDFF: model file is not given
Last message date: Mon Dec 31 2018 - 09:42:31 CST
Archived on: Mon Dec 31 2018 - 23:21:37 CST
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