NAMD-L: By Subject
By Subject
408 messages sorted by:
[ author ]
[ date ]
[ thread ]
[ attachment ]
About this archive
Starting: Sat Jan 01 2022 - 00:55:09 CST
Ending: Tue Dec 13 2022 - 12:14:18 CST
- (no subject)
- (s) Lucy McEvoy wants to share the file input files.zip with you
- /tmp/slurmd/job8440949/slurm_script: line 31: mpirun: command not found
- << Tool to create NAMD input for non biological system >>
- [namd3 alpha9] FATAL ERROR: Low global CUDA exclusion count! (781005 vs 781007) System unstable or pairlistdist or cutoff too small.
- ABF Free Energy Calculation
- ABF Non-Uniform Zcount
- Advice on choice of NAMD to install for CUDA/GPU support
- Alchemical FEP simulation
- Angle parameter errors
- Anvil Purdue
- Applying a force to a molecule in water
- Applying Constraints for ABF Calculations
- Applying pressure on membrane protein system
- Applying unidirectional pressure on a membrane protein system
- Atoms Per Patch Question
- BUG: ReplicaUniformPatchGrid namd-2.14
- Building NAMD3
- Calculation of interprotein contacts between two proteins
- Chain identifiers in NAMD simulation
- charmm-gui namd inputs not working namd
- CheckpointStore command
- COLVAR moving restraint
- Colvar vs. SMD
- Compute atom/residue-based interactions on-the-fly
- Considering switching to NAMD3
- CPU multinode NAMD 2.14 execution
- Creating a New Patch for RNA
- Creating a parameter file for SiC nanotube
- CUDA error cudaCreateTextureObject
- CUDA error cudaMalloc during running namd
- CUDA error cudaStreamSynchronize(stream) and CUDA error in ComputeBondedCUDA
- Customized revision of NAMD
- Decomposing the free energy contributions
- Density over time
- Didn't find vdW parameter for stop type HB1 Error
- Discontinuity in SMD Forces
- eABF run issue: czar.grad file not covering the reaction coordinates
- equilibrating a system using restraints
- Error
- Error compiling NAMD 2.15 Source Code
- Error in Using Tabulated FF
- error while running simulation with NAMD3.0alpha12 and 13
- Error while simulating on NAMD
- Error: [1]+ Segmentation fault (core dumped)
- Error: Constraint failure in RATTLE algorithm for atom 5298
- Fatal error during running FEP simulations
- FATAL ERROR: Atom 1 has bad hydrogen group size. Check for duplicate bonds.
- FATAL ERROR: Cannot specify both an initial temperature and a velocity file
- FATAL ERROR: CudaTileListKernel::buildTileLists,
- FATAL ERROR: sed: can't read restraints/dihe.txt: No such file or directory
- FATAL ERROR: sed: can't read restraints/dihe.txt: No suchfile or directory
- FATAL ERROR: SequencerCUDA: Atoms moving too fast error in FEP simulation in NAMD3
- Ficoll/Dextran CHARMM Force Field
- Force and RMSD Values for TMD
- Fullsamples ABF choice
- Fwd: Error while analyzing testcph.log file by using pynamd
- Fwd: Fwd: nvidia issue with namd12 Debian 11
- Fwd: Irregular spontaneous membrane bending even in the absence of protein
- Fwd: nvidia issue with namd12 Debian 11
- Fwd: Problems with charmm36 modified nucleotides for psfgen and namd
- glutathione, Charmm 36
- GPU requirements for CUDA enabled NAMD
- Gradual heating
- Heating a system or applying force with some function of timestep in simulation
- How can I convert XPLOR-DCD file to plain CSV file
- How could I select a range of ATOMS by using VMD Program?
- how to continue namd md simulation
- How to extract coordinates from trajectories
- How to get best performance
- How to handle large pdbs in namd?
- How to prepare the topology file for nucleotide FEP in NAMD?
- how to properly calculate the interaction between the QM and MM region
- How to qm/mm calculations with NAMD-QChem
- Hybrid FEP topology for Nucleotides
- Inconsistent PMF profile of Ionized polymer
- Interrupted Writing Restart Files
- Issue Combining PSF and PDB Files
- Low performance in SMwST simulations
- mail about Charmm++
- Minimization Crashing Implicit Solvent
- minimization in water not running !
- Missing cphrst file in incomplete run
- MMPBSA Question
- Multiple Jobs
- multiple-walker eABF run input
- MW-eABF error: specified 1 reference frames, but gspath requires at least 2 frames
- Namd 2.14 CUDA not working on Geforce 2080Ti
- NAMD 3.0alpha12 released
- NAMD analysis
- NAMD and VMD programmer positions
- NAMD can not run 5.6 million system with amber prmtop
- NAMD CUDA Error
- NAMD Energy Plugin giving incorrect energies
- NAMD hangs with replica option
- NAMD on apple M1 processor
- NAMD Simulations
- namd slurm error
- namd slurm getting error
- Namd with slurm getting error
- namd-l digest V1 #3272
- namd-l digest V1 #3281
- namd3
- NAMD3 benchmark
- NAMD3 failed to run longer than 4.2μs.
- NAMD3 Multi-GPU features?
- NAMD3 runs failing with no error - XST failing to load and jumping to negative timestep
- NAMD3, GPU and slurm: FATAL ERROR: CUDA error cudaFree
- namd3-alpha13 on CentOS7
- NAMDenergy
- Native and nonnative contacts
- No performance improvement with NAMD 3.0 alpha8 over namd 2.14 cuda
- No xyz and scfp files in QMMM ORCA output
- nvidia issue with namd12 Debian 11
- Optimal choice of NVIDIA GPU to run NAMD3
- Parameters for naturally modified nucleotides
- PBC and Alignment issues
- pdb file from a particular configuration
- postdoctoral position in molecular modeling
- Postdoctoral positions at Michigan State
- Problems to run namd2-cuda on alienware m15 R6
- Problems with charmm36 modified nucleotides for psfgen and namd
- Puzzle with "small molecule" ligand structure in nucleotide environments
- QM/MM CASSCF shows strange symbols in the input file
- QM/MM time-dependent DFT simulations
- qmLSS for Non-Water Solvents
- QMMM analysis on downloaded ORCA /0
- QMMM Question
- QMMM Update
- QMMM write forces for a single step (run 0)
- Query regarding performance
- Question
- question about namd3 performance
- QwikMD QM Tut - FATAL ERROR: Error running command for QM forces calculation.
- RAMD error
- Reading CHARMM36 .str topology error
- Regarding minimization of a protein
- restart glitch - return to original structure
- Restarting a simulation
- Restarting namd-mopac QMMM
- Restraints to maintain shape of particle
- Running NAMD Singularity container on GPU multinode cluster with Omnipath
- S-S bond
- setting forceRAMD
- Simulating a system with an imaginary barrier
- Simulation running slow (1ns/day)
- SMD Question
- SMD simulation
- smd simulation using gaff parameter
- Snakemake with NAMD
- Steered molecular dynamics simulations of peptide with non standard amino acid using GAFF parameter
- The parameter error in the NAMD Energy of VMD
- TIP4P Simulation Scripts
- to rigidify bonds without hydrogen (about suggestion http://jeffcomer.us/downloads.html)
- Tool for Repositioning disordered loop: TMD
- Unable to open binary file md_equ_300.out.rst.vel
- Unable to run NAMD3.0 on 2 GPUs simultaneously
- Use of Targeted MD vs. Colvars
- using amber force field in namd simulation
- Using non bonded energy table option
- Utilizing all GPUs on multi-node environment
- Very High RMSD Value from NAMD Simulation
- weighted ensemble algorithm
- When should I use NTER and NNEU as a patch?
- Where to find top_all36_cgenff.rtf/prm version 4.5?
- Wrong number of p
Last message date: Tue Dec 13 2022 - 12:14:18 CST
Archived on: Tue Dec 13 2022 - 14:32:44 CST
408 messages sorted by:
[ author ]
[ date ]
[ thread ]
[ attachment ]
About this archive