Amber Archive Apr 2018 by subject
- [AMBER] "bad atom type: DU" error
- [AMBER] (pmemd.cuda.MPI) Note: The following floating-point exceptions are signalling: IEEE_UNDERFLOW_FLAG IEEE_DENORMAL
- [AMBER] A Problem about Alanine Scan of Proline
- [AMBER] accelerated MD cudaMemcpy GpuBuffer::Download failed an illegal memory access was encountered
- [AMBER] Aligning frames and printing pdb files
- [AMBER] AMBER Digest, Vol 2256, Issue 1
- [AMBER] AMBER Digest, Vol 2271, Issue 1
- [AMBER] Amber Lipid Force Field Tutorial: update?
- [AMBER] Amber16+AT17: Several checks failing w/Intel Parallel Studio XE 2018.1
- [AMBER] Amber18 and Amber14
- [AMBER] Amber18 and Titan V graphic cards
- [AMBER] Amber94 charges for neutral amino acids
- [AMBER] AmberError: FLAG ATOMIC_NUMBER
- [AMBER] Ambertools17 error: 3D-RISM calculation
- [AMBER] Amino acid GROMACS topology file
- [AMBER] Analyzing Multidimensional REMD Simulations
- [AMBER] Are the equations for FF14SB and FF15IPQ same or different
- [AMBER] Atom position changes when setting up QM/MM calculation
- [AMBER] atomic radius data in amber library
- [AMBER] ATP hydrolysis
- [AMBER] average between structures with different residue numbering
- [AMBER] Boost not linking when compiling on Mac
- [AMBER] Brand new GPU card testing
- [AMBER] Building Amber16 CPU with Intel Compiler and GPU with GNU Compiler vs. MPI
- [AMBER] Calculate minimum distance between two groups of atoms
- [AMBER] Calculate water density in the protein water channel by Amber 16
- [AMBER] Call for Papers, GCC 2018, 14th German Conference on Chemoinformatics
- [AMBER] center of mass restraint in pmemd.cuda
- [AMBER] Changing box size
- [AMBER] Charmm36 modified forcefield in Amber
- [AMBER] Configure cuda
- [AMBER] Configure cuda (David A Case)
- [AMBER] Constant Redox potential MD simulations
- [AMBER] Continuous hydrogen bond time correlation function S(t)
- [AMBER] convert psf to prmtop
- [AMBER] Converting gromacs TRX file to mdcrd.nc and mdvel.nc
- [AMBER] Count water in active site
- [AMBER] Cpptraj and Sander Question
- [AMBER] Cremer Pucker values using Pytraj
- [AMBER] eCheminfo Milano July 16-29, Training and Innovation Course in Drug Design 2018, bursary and early-bird deadline ending soon
- [AMBER] Error compiling AmberTools18 cpptraj with Intel 16
- [AMBER] Error generating gau_job.inp
- [AMBER] ERROR TUTORIAL AMBER --- Step 3.3.3) "Visualizing the trajectories with VMD"
- [AMBER] Extracting forces from the mdcrd file
- [AMBER] Fix for fixed sized cmd in nab
- [AMBER] Forces on atoms
- [AMBER] Fwd: Paramfit issues - Improvement of R^2 value.
- [AMBER] Fwd: Postdoctoral Positions in Computational Biophysics at Westlake University
- [AMBER] GPU
- [AMBER] GTX 1080Ti Problem.
- [AMBER] Help with building a non-standard RNA structure
- [AMBER] Help with mdcrd in VMD
- [AMBER] How can I run PMEMD with multiple distance restraints?
- [AMBER] How fast is Amber's new GPU code? Are CPUs ever coming back?
- [AMBER] How to solve the problem of molecule box jumping?
- [AMBER] installation problem
- [AMBER] Issue running alanine scanning
- [AMBER] Jumping from simulation box
- [AMBER] mac installation problem
- [AMBER] md simulation of modified nucleotides in RNA
- [AMBER] MM-GBSA on pH constant MD simulations
- [AMBER] MMGBSA calculation for complex with two ligangs using three trajectoris
- [AMBER] MMPBSA runs GB but fails in PB for RNA-ligand complex
- [AMBER] MMPBSA.py.MPI TypeError when using &pb
- [AMBER] Multi-Dimensional REMD: rem.log shows exchanges along Hamiltonian dimension, but .mdout files do not
- [AMBER] Multisander: No scale up
- [AMBER] native contacts
- [AMBER] NEB simulations: Inputs from TMD ?
- [AMBER] no output results for heating process
- [AMBER] packmol-memgen and parmed packages import error
- [AMBER] Paramfit issues - Improvement of R^2 value
- [AMBER] Parmchk
- [AMBER] parmed CharmmError: Could not convert dihedral phase to <type 'float'>
- [AMBER] PB calculation is failing
- [AMBER] pH as a Dimension in Multidimensional (2D) Replica Exchange
- [AMBER] pmemd.cuda error; Exiting due to the presence of inconsistent SHAKEH hydrogen clusters
- [AMBER] PMF analysis
- [AMBER] Problem building Amber16 with -cuda
- [AMBER] Problem in disance restraints for atom groups
- [AMBER] Problem with g++ compiler with boost (AmberTools18)
- [AMBER] problem with membrane embedding
- [AMBER] Problem with parallel install
- [AMBER] protons
- [AMBER] Python installation while installing AmberTools18
- [AMBER] QM/MM minimization issue using sander (AMBER 18)
- [AMBER] QM/MM-MD charges
- [AMBER] QM/MM-MD Mulliken Charge calculation output atom name changed
- [AMBER] QMMM Replica exchange with TeraChem
- [AMBER] Query about Constant pH cpout file
- [AMBER] Query for force field parameters of 'R' and 'S' enantiomers
- [AMBER] query regarding nonlinear pbsa
- [AMBER] Questions about SEBOMD with Divide and Conqure method
- [AMBER] RED Server deriving charges for hybrid molecule using GLYCAM ff
- [AMBER] Regarding AuCl force field
- [AMBER] Regarding input files
- [AMBER] Release of Amber18 and AmberTools18
- [AMBER] Replica exchange in explicit solvent
- [AMBER] Replica Exchange: an illegal memory access was encountered launching kernel kClearForces
- [AMBER] residue looks like it is not a part of protein
- [AMBER] Resume AMD simulation
- [AMBER] RNA with Amber16
- [AMBER] Segmentation fault - invalid memory reference, during the minimization
- [AMBER] Simple normal mode analysis in amber
- [AMBER] Simulation between DNA and small molecules.
- [AMBER] Simulation of bilayer with negative pressure
- [AMBER] simulation with duration of 5000 Ps
- [AMBER] Solvateoct Distance Parameter
- [AMBER] Suggestions to pick up right methodology
- [AMBER] superimpose two atoms in cpptraj
- [AMBER] Temperatured-Based Replica Exchange: an illegal memory access was encountered launching kernel kClearForces
- [AMBER] Thermodynamic integration with sander + using nosoftcore
- [AMBER] Thioester Bond:leap
- [AMBER] topology file
- [AMBER] Trouble Running/Understanding Wavelet Analysis
- [AMBER] Two-Dimensional Replica Exchange in AMBER
- [AMBER] Unable to perform MD because of Fortran runtime error: End of file
- [AMBER] variety of errors in membrane/umbrella sampling simulations
- [AMBER] Volume occupied during MD
- [AMBER] Weight the xyz components of restraints
- [AMBER] When did SCEE and SCNB make it into the force-field files
- [AMBER] ZnS force field parameters
- Last message date: Mon Apr 30 2018 - 20:30:01 PDT
- Archived on: Sun Oct 13 2024 - 05:55:38 PDT